I suppose it's possible to visit the small towns of Chianti without a car but it would be inconvenient trying to use public transportation. We have on many trips rented a car in Florence and driven to Siena as a base and toured Tuscany from there. Sounds like you want a rural rental. That would be nice but even harder without a car.

well Tuscanny and Chianti are not exactly the same place so I guess we can be pretty wide in our answers.

From a bike point of view the area is pretty hilly, there are some american bike companies based there who charge an arm and a leg. I'd suggest either do it yourself (I can give loads of ideas if you want) or use someone like headwater (google) it to set up a good tour.

The easy to get to places by train and plane are Pisa, Lucca, Florence and Chiusi. There are other smaller places and I'll et you look at all good rail maps (trenitalia) to pick up some others. However Chiusi is down by some nice towns like Pinza and others ( a quick surf on tis site will offer you loads of choice)

You don't really need a rural retreat as many smaller towns have great places in-town. Just pull up google maps, add agritourismo to the search and have a look.

Once you have good idea of what you like wither use Tripadvisor or come back and ask us which one is best, someone will have stayed there.