I haven't been to Ushuaia itself, but I've just recently gone between Punta Arenas & Puerto Natales. There is a convenient penguin colony you can visit that's a short drive off the main road between the two towns, quite near Punta Arenas, and another colony on an island that you can get to by boat tour from Punta Arenas. If you can manage to get a day in Punta Arenas on the way, there are tour agencies in town that can take you to either colony on a tour. The one you drive to is called Seno Otway (that's the one I visited, though by car rather than tour). The one on the island is called Isla Magdalena. A web search should turn up tour options.
Seno Otway was a lot of fun. It was great to see hordes of penguins swimming and wandering around the landscape. You should try to get to a colony there if you can.
Lisa