Itinerary help please!

Also is it better to book ahead of time or when we get there?

Many people look at the weather before deciding and book things at short notice, though that gets harder in the high peak. Peak arrives towards the end in June, so late in June things might be getting a bit heavy. The Silfra snorkelling is more of a special interest small group tour and I would contact an operator in advance about that. Also ask them how long it takes, etc. The Jokulsarlon trip might not run every day, since demand for this bottom-numbing tour is not huge, so better check out when they run. The tour operator should also advise whether it includes a boat trip, and/or if it is obtainable for a supplement, ie, whether the stop is long enough.

Who should we go with to visit the Blue Lagoon?

There are also public transport options you can investigate, though the distinction between transport and tour is getting a bit thin here - if it is a ticket-and-transport one-price deal they are probably making a turn on your entrance ticket. Personally I'm not interested in going there, but many people seem to prefer it as a leaving treat rather than an arriving treat. Or maybe you could fit it in in an evening after a day tour, they are open late, though that won't be the Jokulsarlon day as you'll be back too late.

You ask about operators, but actually there aren't very many operators for most things, especially the less common stuff. But there are many agents selling the same thing, so you might like to try and identify whether you are looking at an agent's website or an operator. The operators are usually very clear about just what they are offering, but you do have to remember the weather risk.

Ok a little bit of an update...

So we have the option of cancelling our airport transfer to the hotel. SO with that we are thinking of renting a car...

So now the tentative plan is this:

Day 1: Arrive in Keflavik, get rental car, go to Blue Lagoon on the way to hotel in Reykjavik, after checking in walk around Reykjavik.

Day 2: Leave early and drive to Jokulsarlon, spend as much time as possible, go on zodiac boat. Try (now I'm going to look) to stay somewhere cheap in Skaftafell (because we're still paying for our hotel in Reykjavik).

Day 3: Drive back to Reykjavik but stop in Vik along the way (see black sand beaches, Dyrholaey, Myrdalsjokull glacier) and anything else that is on the path back to Reyjavik (will take suggestions here!!!)

Day 4: Drive the Golden Circle tour (see Thingvellier, Geysir/Strokkur, Gulfoss, Kerid (??? worth it??) AND schedule a snorkeling trip in Silfra (suggestions on who to book this with??). Anything else we can include in this day or we should see during this day?

Day 5: Go back to airport/return rental car

Anyway to add in Snaefellsness peninsula?

Hi!
I would doubt the Day 4 – Golden Circle is approx. 300 km, and you will definitely make stops along the way to make photos, to walk, to stay in queues to some sights – will snorkeling trip be a good idea after quite a tough day?
Here is a nice table with car rentals http://www.iceland24blog.com/2013/05/rent-car-in-iceland-car-comparison-by.html

And have you considered Landmannalaugar? http://www.landmannalaugartours.com/

to stay somewhere cheap in Skaftafell

Accommodation isn't cheap in Iceland unless you bring your own sleeping bag and sleep in hostel standard accommodation (often called SBACC - some guesthouses offer it as well as hostels), or camp. At Skaftafell, there is only a campsite or a hotel. The guesthouse has closed. Maybe there's some guesthouses opened up about 10-20km E, because there's a scatter of buildings there and maybe someone thought there was some money to be made. Or go back to Kirkjubaearklaustur.

Why don't you keep Jokulsarlon for your next visit when you have the time? I didn't see Jokulsarlon on my first visit to Iceland, and that was a 17 day visit. Nevertheless what I did see was great enough I went back several more times, and have now seen Jokulsarlon twice, (and the weather was poor both times...) There's so much that great's you can afford to keep some great sights for next time.

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