During a rainy day visit the Deutsche Museum. The German version of the Smithsonian. Great place for your boys.

Transport into the city is easy by train. Takes about 45-50 minutes. A taxi is very expansive because of the distance and you might get stuck on the autobahn especially during rush-hour.

Restaurants are no problem. 99% of the restaurants are completely smoke free. Just pick a Bavarian restaurant downtown like Augustiner, Paulaner. Just stay away from the Hofbräuhaus. This is in my eyes just a bad tourist trap.