Best place in Boston that I can think of is the paved pathway that runs along the esplanade. It has some grass on either side, good for falling, and usually isn't that crowded, especially earilier in the morning.
In Cambridge on the weekends, there are quite a few side streets in the neighborhoods between the Galleria and MIT that are fairly, if not totally devoid of traffic.
If you're just practicing, Boston Common and the Public Gardens should offer plenty of areas to ride, again it would be better eariler in the morning. You won't get alot of distance work in, but it's a good place to enhance you're skills, with lots of paved and unpaved riding area.
I wouldn't sweat taking my bike on the T, it's allowed, the other riders will get over it.