i live in brooklyn, and it'll be a 1.5 hr commute each way for me, but as i've said in other posts, i have my reasons for staying in the BK. i'll take the subway -- the 5. for me, i take a local train 3 stops, like 5 minutes, and then transfer to the 5, and it's a straight shot. long, but i'll get a seat, and a monthly subway card is $81 bucks. it's a 10 minute walk from the 5 to campus -- unless the weather is really awful or you have bad knees or something, there is no need to take a bus from the 5.
transferring bunches of trains and buses is a pain, but as long as you keep subway lines in mind when you look at neighborhoods, there is no reason you have to transfer, or transfer more than once. i and other posters have posted links to subway trip planners -- those may be helpful.
you can definately live closer and have a shorter commute. feel free to pm me, but there are lots of less expensive (in NYC terms) nabes. ones that are closer to AECOM are many parts of the bronx,of course (morris park is nice, as are other bronx nabes. i am not an expert on the bronx, but the areas i've been in and like are cute family type nabes -- not hip, not a lot of bistros and boutiques like you'd get in brooklyn and manhattan and parts of queens, but safe and not expensive). east and west harlem and the UES are also more affordable parts of The City and will not be a bad commute.
i have many ties, social and $$ to brooklyn so i'm staying here, but if i were moving i'd totally look at living in the bronx. you're going to be at school all the time anyway, so why not let your money go to a bigger nicer apartment, since the bronx is more affordable, and let your time be spent, well, not on the subway. just my 2 cents.
i don't like the express bus because i get really carsick, and if i'm going to be on transportation that long, i want to get some reading done. also, it may be called expresss, but you are still subject to manhattan traffic, which can be a nightmare. but it is very comfortable (especially if it doesn't make you sick -- then you can go to sleep on it!), a/c, clean, and more civilized than the subway, and i know lots of folks who like those buses. as you have discovered, it's about 2x as expensive as the subway pass.
i don't drive. like, i never have. you don't need to here. BUT if you live in the bronx or the right nabe not in manhattan, it may be worth it. be warned, parking can be a bee, traffic may rob you of all altruistic motivations, and insurance in NYC is some of the highest in the country. people i know who have cars to travel between outer boroughs seems to find it most worthwhile -- like if you decide to live in riverdale in the bronx (nice area!) or somewhere in queens. but listen to others over me. my BF drives and manhattan driving makes him very unhappy. at the same time, 1/2 my friends keeps cars (all live in BK) so there must be something to it.
congrats on med schoo!