It will be very crowded. We have done the whole week of Thanksgiving including the days you are considering for the last three years. There's not really going to be much difference between your day choices, but I might actually go with the Sunday/Monday. Yes, weekends are very busy, Sundays more so than Saturdays, but during Thanksgiving week, I feel that the crowds just keep building and building until they peak on the Wednesday. I think Sunday afternoon/evening will be pretty busy, but Sunday morning might be less busy than Monday or Tuesday morning.
From your post, it sounds to me you may be on a bit of a tight budget. If you can afford to spend a little more though, I would consider at least one of the following. Skip the hotwire hotel and take a look at walking distance hotels on Harbor, pretty much anything from Hojos on the one side of the parks down to Candy Cane Inn on the other. I don't have the map link right here, but it's probably on one of the stickies at the top of the page. You will have a better ability to get to the parks before opening, afternoon breaks will be easier if you can just walk back and forth, and you won't be spending extra time and hassle dealing with transportation options. Two days is going to be really short. You might want to bump your tickets up to three days. This will also get you access to magic morning one day which will be useful if you can get your teenager up and to the lines at the park gates before 7 AM on the Sunday or Tuesday morning. Having three days in the parks will give you enough extra time that you could afford to lose a little more time to transportation and choose a cheaper further away hotel if that's where you want to save money. Whether you go with two day or three day tickets, make sure you choose parkhoppers so that you can go back and forth between the parks each day and maximize the time you do have.