but in the end, the two hours that the commute takes out of your day really wears on you.
I'm so glad I don't have to put up with the MTA's nonsense beyond Bowling Green.
Can't speak for the Williamsburg area, though I'd be nervous about the L train being your only access to school.
I obviously can't give input about NYU D2, as a D1 myself, but as someone who has lived in the further reaches of Brooklyn (New Utrecht off the R line), and the middle reaches of Williamsburg (Montrose Avenue off the L line), I just wanted to add a few things.
As of 3 years ago, the L train is good and getting better. Generally speaking I rarely had trouble taking the L where I needed to go - there were a few random nights when I would have to wait up to 20 minutes for a train, though, and a few nights where the L wasn't running so I had to cab home, so be prepared for random frustration. But these nights were rare - I think 3 out of the school year that I lived there. If you can find a nice place in Williamsburg, the L train is nothing to really be afraid of.
Side note: The rent was ~1600 for a railroad, so not the best deal we could have gotten, but thanks to our d-bag of a previous landlord deciding they wanted to keep their apartment free for their new baby with less than 3 weeks notice before school started, we were in a rush.
New Utrecht (the previous site) was another story. It was like an hour out there, and rent was like... 1050 combined, for the upper floor of a house - full living room, master bedroom, full kitchen, study, and (very) small bedroom. I will say that the commute wore me out very quickly, even in the summer when I didn't have work to do. All of these lies about "You can just read on the subway" or "Study on the subway and you don't even feel those two hours"....yeah, you will feel them. Trust me; unless you are some sort of benevolent god of focused studying, you will feel them.
This all said, keep in mind that if you are walking distance now, and subway distance later, you will need to pay 125 or whatever ridiculous amount every 30 days for a Metrocard, so you need to factor that into whatever rent you're saving. If you think 125$ + 1+ hours per day per month translates into a better deal than staying in Manhattan, then I wish you good luck!