I visited the museum, called Rocca Al Mare or in Estonian, Eesti Vabaohumuuseum, in early Sept 2013, and it was quite interesting--I have Estonian heritage so it was particularly satisfying for me to see the houses and examples of how people lived throughout the centuries, with English translation. It's quite spread out, very pretty and peaceful (probably busier when you'll be there in June), basically an enormous park with pathways and you can rent a bike if you're so inclined--I just walked. It's along the Baltic and I spent a bit of time picking up sea glass. There's food available and a small gift shop with some beautiful handcrafted items. I allowed 2-3 hours, and from there walked about 25 minutes to get to the zoo. Nothing special there, but it filled out my day nicely--I spent a week total in Tallinn, and I highly recommend the Kadriorg Palace, as well as the nearby KUMU, modern art museum--easy tram ride from old town area.
Getting to the open air museum was a bit of an amusing ordeal for me--I set off with directions to the bus, walked and walked and couldn't find the right stop, and everyone at the bus stops seemed to be Russian--lots of them in Tallinn and none seem to speak English though the Estonians I encountered all spoke it very well--I'd ask about the bus and they'd just look me up and down curiously and shake their heads. Finally I headed to a nearby hotel to catch a taxi out there. Again with the Russians. Several drivers conferred and one got the honor of transporting me. It was about a 10-15 minute ride, and every few minutes he'd say in a reassuring tone, "Rocca Al Mare!". Based on my map I knew he drove me straight there, and I don't recall the cost but it wasn't much. After the zoo I did catch the bus back to Tallinn proper. You might be better off just taking a taxi, especially if time is tight for you.
If you have from 9-5:30 I'd say allow a couple of hours each at Kadriorg and Rocca, then back to old town to do your walking tour--old town is nice and compact, and it's delightful to wander the little streets, gorgeous buildings and views, lots of touristy shops but also quite a lot of ones featuring handcrafts from Estonian artists, particularly along St Catherine's Passage. I'm not sure where the cruise ships dock but I did take the ferry to Helsinki and the taxi ride there was about 10 minutes.
I hope you have a wonderful time--Tallinn was my first medieval walled town and I fell completely in love with it and hope to return in the next year or so.