There are plenty of great hotels.
Zurich: Baur-au-Lac (the best one in the city), Central, Schweizerhof
Luzern: Palace, National (the latter has great sport/spa facilities)
Getting there from the airport is easy - the trains are departing every few mintues and are very comfortable. If you buy a ticket between airport and the city, it is valid for all kinds of public transportation (trains, buses, trams, even boats!) for 2 hours.
First thing you should do upon arrival into the city (both Z. and L.) - find a tourist infomation offce at the main station (there are sign overall, showing how to find it). They can sell you a City-Card (valid vor 24, 36, 72 hrs) for unlimited travle by public transportation and free (discounted) entrance into dosens of museums etc. They will also provide you with all info, maps and like - everything for free.