We were just there in July. We did not see the city museum. My expectation is that it is a typical sterile stuff/mount display. The city streetcar system is worth a ride. Lots of 1960's era steel motor/trailer equipment with juice jack pantographs. One line has gauntlet track. Another line makes a steep ascent of the hill near the castle. The tram museum advertises excursions on wooden single truck equipment, and we actually saw this equipment on the street. The tram museum advertises in tourist guides.
Instead, we went to the state museum in Luzna u Rakovnika. I recommend it. It is a Czech "Steamtown". Fully functioning roundhouse with many locomotives maintained running. They also have a tiny loop of 600mm track for kiddy rides behind diesel or steam tank engines. There is also a private museum in Knezeves (nearby the state museum). The steam excursions run on an out of service branch between the two. Equipment alternates between state and private sources. The trip includes an hour stop at the private museum where lunch (sausages) can be purchased.
The trip is a lot of fun. Buy bottled beer at the station vendor for the trip! No limit on open platform riding. Note that English tourists are rare, and nothing is in English. Basic web information is in English, but train schedules are not.
http://www.cdmuzeum.cz/
The trip from Prague to Luzna is about 1 1/2 hours each way by train. The Thomas Cook timetable is not detailed enough. Use the Czech railways website http://www.cd.cz for trip planning. Some trips are faster than others. Lines west make a long slow sweep of the city. Look for a station en route closer to your hotel.
About Prague: we did not really enjoy the city. Crime is a problem, and you are constantly warned about pickpockets and deceitful taxi drivers. Limited areas are attractive, with the rest still looking like Soviet times. There is a paddle steamer in Prague, but you have to speak to the office in Czech to learn which trips amongst the diesel boats it operates.
The suburban and regional services are amazingly efficient and clean, with new or refurbished diesel multiple unit stock.
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