The Science Park stop on the Green Line is not Handicap Accessible so if you have a stroller be prepared to take it down (and up on the way back) a few flights of stairs. You can buy a Charlie Card at the T station it is cheaper than paying for a paper ticket, kids under 10 ride free. The Red, Green, Blue and Orange Lines run every few minutes, the Purple (Commuter Rail) runs less frequently.
Some other places to visit that are one the T are
Boston Children's Museum- South Station -Red Line
New England Aquarium- Aquarium- Blue Line
Boston Public Garden- Arlington St- Green Line
Frog Pond and Tadpole Playground- Park St- Red Line
Not sure how old your children are but my 5 and 3 year olds love those spots :)
You can use the trip planner on www.mbta.com