Tampere has an interesting set of museums in a former industrial site,
Museokeskus [Museum centre] Vapriikki
But for two days arriving in Helsinki, i suggest finding an out-of-the-center hotel and just looking around Helsinki. The public transport is good. Things to do include Suomenlinna, Seurasaari open air museum (after 15 May), the city architecture history museum, the Design museum, the National Museum, walk along the streets around Esplanadi, etc.
If you want to go and stay in Taliinn for the night, I suggest taking the ferry there and sleeping onshore in a hotel, rather than sleeping in the ferry when it's docked at the quayside in Talliinn. Not only do many people get off when it arrives, undoubtedly noisily in the middle of the night, but you have to get out by 07:00 the next day anyway. Not the sort of night sleep I would like.