Taxis are okay, but as stated earlier will be on the expensive side and take awhile, depending on traffic. And there will be traffic, just to what extent.
Air Train to LIRR and then the subway works, or Air Train to Penn, can from Penn to TS. I used to work in the subways, and while perfectly safe in mid town, I just hated them. That's why i say cab.
I'm not an architecture type, but definitely check out Grand Central (The whispering wall fascinates me). Go down town for the older buildings. Wall St is nice, Broadway (where the Wall Street Bull is), and anything around there.
I've never been on the tour busses, but I'd suggest "The Ride". Dealt with some of the others (Big B and Hop on/off) and was less then impressed.
If they need anything during their stay PM me, I work in the city and can help point them in the right direction if needed.