Hey there, future classmate. I can give you my advice from my apartment search (which thankfully is done...), but some Bostonians may be able to pitch in and supplement what I say.
So, I scoured CraigsList and set up meetings with brokers. A broker is the most convenient way, but you're going to pay for that convenience. The fee they charge is equal to 1 month's rent, and sometimes the future landlord will pay half of that fee so that you only have to pay half yourself. Sometimes they'll pay the whole thing if you get really lucky. Brokers will be able to show you many different apartments in all kinds of neighborhoods, and they can do that in a short period of time. I toured about 6 apartments in about an hour and a half when I talked to a broker. You are allowed to tour with no obligation to rent a place or pay them for the tour, by the way.
However, I didn't want to pay a fee, so I spent some quality time on CraigsList searching for "by owner" and "no fee" apartments. You have to sift through a lot of apartments, many times apartments nowhere near where you wish to live. This is how I found my apartment, though, so it can definitely work.
As for prices, the neighborhoods you mentioned are very comparable in price, though Brookline is a bit more expensive. Generally, the closer you are to the T, or to "hotter" areas, the more you'll pay. Then of course, different amenities within the apartment can raise the price (such as a dishwasher, or reserved parking spots). Studios generally ran from 900 at the very low end, to about 1200 at the higher end. 2BRs were anywhere from 1300 at the very low end, to 1700 at the higher end. I chose to live in Allston, myself, and found a place with reserved off-street parking. If you don't plan on bringing a car, I would recommend you live as close to the B-line as you can afford to, though.
I wouldn't think that the end of May would put you completely out of luck for a July 1 move-in date, especially not if you looked on CL. However, July isn't a common date for leases to begin -- most begin on Sept 1 in the student-populated areas. You can still find some July 1st apartments though. In general, though, the sooner the better - especially in neighborhoods where tons of students are looking for about the same thing as you are.
As for finding roommates, I'd say you should wait a little bit (not too long though) to see if they can finalize their plans. However, if they did end up having to drop out on you, it would not be difficult to find an acceptable roommate.
Hope that helps you a bit, lemme know if you have other questions.