My 4YO son has 2 different Thomas sets and several GeoTrax sets. He loves them all. We have the wood track Thomas trains which also work with brands from Wal-Mart & ToysRUs. We have the Take-A-Long Thomas sets with the grey plastic track. And we have several GeoTrax sets. (He has lots of grandparents, aunts & uncles.) Anyway, here are the pros & cons of each.
The wood track system has the most add-ons available by a huge margin over the other sets. Plus there are compatible sets available in several brands, making the cost less. You don't have to have a train table for them. We don't. We keep them in bins in his room and pull them out to play. He's been playing with this set since he was about 18 months. It's easy for him to put together and take apart and there are many add-on packs of track, buildings, trains, etc. The track is extremely durable and most pieces flip over to be used on either side. One drawback, the painted wood trains are more suseptible to wear than either of the other 2 sets. The paint can get chipped or worn on the corners if your son tends to throw or drop them, but they still operate fine. My son is pretty careful with his, but even so, he doesn't seem to care if they are worn and plays with them anyway. These sets will stand the test of time and still have value when your son is throught with them.
The Take-A-Long Thomas sets have 2 different types of track and you'll need adaptors to work between the 2. It's more difficult for my son to put the tracks together himself than with the wood track. There are no other compatible brands. The track seems durable enough, and the metal trains are extremely durable. Great if your son likes to take toys with him places. I know Walmart and Target carry these, and probably some others. I can't remember if ToysRUs has them or not.
The GeoTrax set track is very durable. My son can put the track pieces together by himself, but needs help with the bridges, ramps, switches, and such, like those that come with the Central Station. It's more complicated than he can do on his own. There are way fewer options for trains than with the wood sets. The wheels on the trains are plastic and prone to wear or nicks when dropped, which then can cause problems with running. My son does love the remote and that the trains move on their own and they will run without track, but stay away from running them on carpet. He also has the flying airport and likes it. There aren't many track add-on packs to make all the systems connect together without major calculations on Mom or Dad's part, and no other compatible pieces made by anyone other than Fisher Price. The buildings, track, and trains are somewhat bulky and hard to store. Not such a good deal if your son has a small room. My son just got this for Christmas last year (at age 3) and has added more sets since then. He is very good with trains, tracks, and other mechanical things, but I think it would have been frustrating for him when he was younger.
Depends on exactly what you're looking for, but I would definitely stay away from the blue plastic battery operated Thomas sets. The track is flimsy and the trains are cheap plastic. Not durable enough for young kids your sons age.
Hope this helps!