Both Budapest and Bratislava, I would say definitely deserve at least a day. I have been to Budapest myself and it is a stunning city with plenty to do for much longer then a day, but you can do an overview of the major sites in a day and get a feel of the city. While I have never been to Bratislava, I have heard good things. It is very close to Vienna, so it may be doable as a half day trip. It depends on what and how much you want to see. However with only 3 1/2 days in Vienna, I would recommend doing only one day trip since Vienna is an amazing city where 3 days is a pretty short time to begin with. This site gives information about travel to Bratislava from Vienna: http://www.bratislavahotels.com/bratislava-vienna-budapest-prague-travel

As for Budapest, I would recommend taking the train since they are directly connected.

Bratislava is only 1 hour away from Vienna, have been there twice using both bus and train.
Most convenient was the bust trip, busses are living from Südbahnhof almost every hour, last bus from Bratislava to Vienna was living around 8 pm.
I liked Bratislava very much, it has a beautiful old city and plenty of things to see, you can spend easily 1 day there.

At the most with your limited time for Vienna, I think you could do Bratislava if you didn't prefer another nearby Austrian city along the river. Budapest is too too far to even consider for a day trip.

I agree than Budapest is way to far for a day trip. I would do Bratislava and visit the beautiful villages in the countryside surrounding Vienna for a day, and then spend one and a half day in Vienna.