Short trip to Uganda with a three-year-old

I haven't been to either of those, but if you want to combine a bit of safari with chimp tracking, then you could also go to Queen Elizabeth National Park. The Chambura gorge which is right next to the park does chimp tracking. At QENP there is obviously the game driving but also boat trips on the Kazinga channel where you get quite close to hippos, elephants and buffalo in the water. We stayed at Mweya Lodge (http://www.mweyalodge.com/).

QENP would also be easier then MF to combine with gorilla tracking in Bwindi, although the age limit is 15 for gorilla tracking so you couldn't take your 3 year old. There are plenty of forest walks though.

Oh, yes and kids would love this place which you can do as a day trip from Kampala:
http://www.ngambaisland.org/

In my opinion, Murchison Falls is a much better place to go with kids than QEP. In addition to all in QEP, it has:
- the Nile, with the big crocs, fat lizards and abundant wildlife, all the way to the bottom of the falls / the cruise on the Nile cannot be compared with that on the Kazinga.....!
- the falls, which are amazing
- the chimps
- easily done through Red Chili Backpackers from Kampala

If going to QEP, avoid Myea which is really for those that have a fat wallet. Stay in the brand new Kingfisher, overlooking the whole park.

I would neither go to Kibale....try Jinja, Sipi, Lake Mburo.

Mmmm have to agree with stokeygirl... QE is (with private transport) easily combinable with Bwindi and even with Kibale if you have the time. (That's what we did: Kampala - Kibale - QE - Bwindi - Lake Bunyoni...a quite 'complete' trip I felt)
In QE we stayed in the cheap guesthouse right next to Mweya lodge....but always had our breakfast and dinner @ Mweya.
And that was not so expensive as one would think. Like this we spend little on accomodation but spend our free time (between the game drives) mostly in the gardens of the Mweya :-) Which has a very nice location overlooking the Kazinga.
The boat trip in Murchison will probably be more spectacular, but on the Kazinga we also saw croc's and all the other wildlife including dozens of elephants coming to drink and (which was for us a highlight as we missed that in our Tanzanian safari)....a leopard.
The guesthouse (and the Mweya) are surrounded by bush, lots antelopes (water bucks mostly) etc... are running around everywhere around you. One morning we woke up, I was going out for my morning smoke (it was still darkish) and bumped into....a dead hyena! Killed by a lion that night...that was on 20 meters of our room :-)))
In Kibale we slept in what was called 'the Treehouse' behind the Park office, beautiffully isolated in the woods. Liked that! The first night we spend at one of the lakes between Fort Portal and Kibale, but I preferred sleeping in the Park. Chimp tracking was easy in Kibale and it was really 'tracking'...following the group...must be soooo exciting for a 3-year old!

Have fun, Uganda IS amazing!