Assuming you're staying in the city, TSA will be closer. But TPE is very easy to get to on a very comfortable train, and while it's a big airport, it's also easy to deal with - it's no JFK or LHR.

I'd choose the flight with the best price/timing for you and not worry about the airport. Either one will be fine.

And enjoy Taipei - it's a great city, and Taiwan is a great country! One of my favorite places and one I'm very eager to return to soon. Oh man, the fooodddd....