I took the flightline shuttle MHT-sullivan Station and it was great.
Picks u up at MHT and then just takes you to Sullivan Station where it is a short T ride to downtown and or BOS. Total cost probably 19+2 = 22 ish.
They may ask for tip in the online reservation system but I remember you can just put down $0. I like to give my tip in cash anyway so I know that the drivers are getting their full share.
I do remember the website as not as intuitive but basically it is booking from MHT to Sullivan station or vice versa.
Let us know if u are still having trouble.