Hey Mindy...I'll try to help you out, much of your decision will be based on what hospital you are at.
If you are at the Brigham, or the BI then I say Allston, Brighton, or Brookline, also consider back bay. Alston and Brighton are very student oriented, louder, more undergrads but more affordable with plenty of nice places (resonably priced for Boston). Allston and Brigton are along the "B line" of Bostons green line subway system. Brookline is essentially next door to the longwood medical area. Easy to walk, bike, grab a bus or drive. More suburban, more expensive but less noise and still close to the city. If you think brookline try to get a place in Washinton Square or near Coolidge Corner...both great places with lots of apartments.
If you are at MGH think beacon hill, harvard or central square and back bay. Beacon hill is right next to MGH but it is expensive and the places are very small. Harvard and Central square are right along the Red Line and so is MGH so public transport is easier. Again back bay which is essentially right in the middle of the city and thus central to every hospital.
If you are at BU think South End and Back Bay. South End used to be the pits, a number of years ago, but it is now the hot, up-and coming area and thus it is difficult to find affordable housing, but it is still possible. Lots of places in Back bay and access to BU is easy, but Back Bay is somewhat expensive.
As for cars.......its a nightmare....often places don't come with parking, or you pay 100 or 200 dollars a month for a spot. You will likely also have to pay a monthly fee for parking as a resident. Just give it your best shot to get a place with a spot or even two..they do exist. By the way, driving in boston....its what they will make me do if I get sent to Hell...its worse than LA, but public transport is fantastic, just may not run at the hours that we keep.
Finally another alternate is Jamaica Plain or West Roxbury. These "suburbs" are just past Brookline. The housing is cheaper and you get more. There is also plenty of parking available with your place. SO if you are married, don't necessarily need to party every night in Boston, but still want to be very close, this is a great place to look.
If you are coming from out of town, it might be a good idea to use a realtor, yes it is one months rent paid for nothing, but it may make it easier and the agent can continually send you stuff over the internet or e-mail. Good luck, any more specific stuff, just drop me a line and I'll try to answer.
Ca. Dreamin'
