Both SE Asia itineraries are great, either north Vietnam plus Laos, or south Vietnam plus Cambodia. If you decide on the first one, you'd need to fly from Hanoi to Luang Prabang, which is not expensive. There's no way you could survive a minivan trip all the way from Hanoi over the mountains into Laos with your sanity intact, going with a 5 month old baby.

Shorter is probably better if it's your first time traveling with a baby. In 3 weeks you can get a good taste of SE Asia. To help you choose a route do some reading. Either get a copy of the LP SEA on a Shoestring guide, or there's a lot of free info on the region at www.travelfish.org .

Yes - there is a vehicle ferry (of sorts) across the river. You'll need wheels of some kind - rented or driven - and you can follow the river down or up. Last Time I was there, there wasn't much in the way of signing, I just drove about to see what I could see.

https://www.google.com/maps/place/Vehicle+Ferry+Landing+North+Shore/@19.8946322,102.1302518,3a,75y/data=!3m8!1e2!3m6!1sAF1QipOEiLkyvNtfMD5y8hDP9xglZvfwo6Mkxm8lSEYZ!2e10!3e12!6shttps:%2F%2Flh5.googleusercontent.com%2Fp%2FAF1QipOEiLkyvNtfMD5y8hDP9xglZvfwo6Mkxm8lSEYZ%3Dw176-h86-k-no!7i2543!8i1236!4m8!1m2!2m1!1sferry+luang+Prabang!3m4!1s0x312f2a68a3e132eb:0x58dcaaf951a372de!8m2!3d19.8946322!4d102.1302518

I took the regular two-day slow boat from Luang Prabang to Huay Xay last week and noticed a sign in the back of the nice boat saying they also operate for charter with the name Mekong Smile Cruises. Google turned up this link - http://www.mekongsmilecruise.com/ . I suspect you could charter this boat for a few days at reasonable cost in the slow season. The boat was super clean and run by a family with the young mother in control. Nicest boat I’ve been on and even had separate western toilet rooms. No sleeping cabins though but I’m sure they could hang partitions as it’s a very long boat.

So far as I know, the only thing that can be called a "cruise" in Laos is the 2 day tourist boat between Luang Prabang and Huay Xai on the Thai border. Starting from LP is more enjoyable since the boats won't be nearly so crowded. Because most tourists start from Thailand.

So far as the rest of Laos goes, bus travel is the most economical option available. If it were cheaper than buses, Lao people would use boats on the Mekong river to go places. But they don't do that. So no boats go from Vientiane to Tha Khaek, etc.

First bus from Luang Prabang southern bus station to Vientienne, with the schedule here:
https://www.hobomaps.com/TravelLuangPrabang.html

And then from Vientienne southern bus station to Thakkek, bus schedules on the link from poster #4 :
http://hobomaps.com/TravelVientiane.html

Note: Your bus from LP will arrive at Vientienne northern bus station, so you'll need to transfer.

It would make more sense to fly in and out of different places, if you have not yet booked flights. Backtracking is a waste of time, unless unavoidable, and is very limiting. If stuck with a return flight to/from Vientiane, you might want to look at stopping off between Vientiane and Luang phabang, rather than heading any further north. I would recommend Nong khiaw and Muang ngoi, but the further you go, the longer the journey back to Vientiane.

For me, a good 2 week combination of the 2 countries would include Phnom Pehn, then Siem Reap/Angkor Wat on the ground for at least 3 whole days, then bus overland into Laos from Siem Reap, stopping once you cross the border in the 4000 islands region (Nakasong/Don Det/Don Khon). Then 2-3 days there to include Champasak ruins, and fly out of Pakse to Luang Prabang. And spend the rest of your time exploring LP and nearby places in northern Laos.

There are variations on this theme, of course. But if you want to include a beach island in Cambodia, it's hard to see how you'd have time for anything in Laos other than Luang Prabang.

Dear murkinavasu,

thank you so much! We did a lot of research for exactly this Route: From Thanh Hoa to Sam Neua via Na Meo border crossing. Most information were really outdated.

Thanks to your post we felt much better giving it a try.

Everything worked as you described.

We (a german couple) slept at Thanh Hoa near the Western bus station 'Bến xe phía Tây' [https://goo.gl/maps/EADhGVt9ut9xBnWv9]. In the morning we took a taxi for 30.000 VND to the bus station. We arrived at 7:30 a.m.. We asked the driver about the price and were told 500.000 VND/pax. The bus left at 8:15 a.m.. Later at the busdrive we were asked to pay exactly that price. Touristprice but no scam. (We observed that locals paid 200.000 VND).

We seated our selfs directly at 7:30 a.m. on two of the free seats. Good idea. Around us the bus was crammed with lots of cargo and more people than seats.

At the Border Crossing Station Na Meo [https://goo.gl/maps/pCsieeh8f74xRmZK8] it was no problem to exit Vietnam at the vietnamese border, even though we had an vietnamese eVisa, also the entering to Laos was no problem with a Visa-on-arrival.

We got official information concerning the depature at Na Meo on vietnamese site (with eVisa) from:
https://evisa.xuatnhapcanh.gov.vn/

Official List of ports that allowed foreigners enter and exit vietnam by vietnamese eVisa:
https://evisa.xuatnhapcanh.gov.vn/documents/20181/117155/List-of-evisa-port.pdf

An useful even though not official map of Bordercrossings / Landports in Vietnam:
https://north-vietnam.com/border-crossings-in-vietnam-map-enter-exit-with-e-visa/

We got official information concerning the arrival and immigration (as well as information concerning Visa-on-arrival) at Na Meo on Laos site from:
http://immigration.gov.la/checkpoints/

[Please check carefully if the option for Visa-on-arrival still exists at 2020].

Departure at vietnamese site: Fast and without any fees.
Walking to Lao-Border-Immigration.
After a short checkup of our passport we got an immigration card to fillout. We needed one passfoto and had to pay 40 USD/pax visa-fee.
After a few minutes we got back our passport with an visa and one stamp.
We even could change our leftover VND to LAK. The exchange rate was acceptable.

The busride continued. Everything went well and without bad surprises. Nevertheless the 9,5h procedur was exhausting. The road wasn't always in a good condition. Lots of serpentines and not always paved.

When we arrived at Sam Neua 'Na Thong Bus Station' [https://goo.gl/maps/MvVc3kPwSVAQVhSr9] one taxi was waiting. We were very lucky one of the bus-passengers took us for free with her privat car to Sam Neua.

Additional Information for Sam Neua:
We slept at 'Bounhom Guest House', [we couldn't find it on googleMaps, or booking, but on tripadvisor]. It is located next to 'Dan Nao Meuang Xam Restaurant' [https://goo.gl/maps/w6JGtmpvWhbEB9yHA] where we liked the food a lot.

Additional Information for traveling on:
The next day we took the bus in direction of Vientiane, via Nong Khiaw and Luang Prabang from the 'Phou Tanou Bus Station' / sometimes called "Upper Station" [https://goo.gl/maps/GTbgXy74jfzLx6w26] at 7:30 a.m.. The schedule we found at hobomaps [https://hobomaps.com/TravelSamNeua.html] seemed to be up-to-date. Be aware that you find a lot of different and sometimes outdated schedules. There is a tourist information available in Sam Neua. Best to ask there!

I mean the bus won't originate in Muang Khua, nor will it pass through there: the bus will originate in Luang Prabang. I believe there might be new roads in the region since I was last there, so I don't know what the name of the junction point is. But if Pak Nam Noi is on whatever the current main Luang Prabang-Phongsali road is, then yes, the buses will pass through there. I wouldn't really recommend night travel by bus in Laos though. The roads - especially in the north - are dangerous enough during the day.

I think it's very unlikely that a road has been built from Muang Ngoi to Muang Khua, so yes, a boat is probably your only option on that stretch.