Hi there. We are going on our first family trip to Disneyworld in just a few short weeks. It will be just my husband and my 3 year old (almost 4 in January) daughter so we are a similar traveling family as yours.
I would definitely pick Disneyworld over Disneyland. There is much more to do at world because there are FOUR major theme parks: Magic Kingdom (which will have the most for your son), Epcot, Animal Kingdom and Hollywood Studios.
My biggest tip, especially if you have a tight budget, is to go during the "Value" or "Off" Season. I'll include some links so you know when that is but when we're going Dec 11-17, that is part of the Value season. November through the 1st two weeks of December, excluding Thanksgiving week. Also, in late Aug through early September is also a part of the Value Season because kids are back in school. Basically, eliminate any holiday weekends/weeks, Spring Break or any time during the summer. And Disney will sometimes offer their Dining Plan for FREE during their Value Season which is what we got for this trip and is saving us a TON of money. But they basically only offer it during those times so that is the BEST time to go. You didn't say how far out you are planning to go, but planning now for an Aug/Sep trip would be great. And you don't have to worry about his school schedule being interrupted. Also, the crowds are better and weather is more pleasant.
Here are some great websites:
mousesavers.com
They have a TON of information and great tips on going with kids. They can take you step by step through the planning stages. On the left-hand column, look under "Disneyworld" and then after you click that, there are lots of tips listed in a menu such as "How to get started", etc. and there's lots of great advice.
disney.com, then click "Parks" at the top
This is obvious but there really is a lot of great information here, especially pictures, video, etc. and you can get a good feel for different places to stay. Also a great place on this site, if you go to "Disneyworld" on the left side when you are on the Parks page, then to "Plan", then to "Moms Panel Advice" - GREAT place for info from veteran Disney moms.
allears.net
Great site.
disboards.com
another forum site where you can search by topic
My next biggest tip would be to STAY ON DISNEY PROPERTY. This is especially helpful with pre-schoolers due to their nap schedule. It is really nice to be close by so you can go back to your hotel. If you stay on property, you get free transportation around the parks, and to/from the airport. There are Value resorts (lowest price) on property up to the nicest suites. You can find something in your budget.
I'd be happy to share more tips with you via email. [email protected]. Happy planning!
Robbin