We just returned from a spur of the moment day trip to Colonia. As such, we hadn't done much research on options for the trip.
Buquebus and others seem to offer tours of Colonia in addition to the ferry transport. The hop on hop off bus costs US$25 per person. We took a taxi from the terminal to the center of the historical area. The fare was US$5, which seemed steep. Going back we used the meter and it was somewhat less. The taxi driver wanted to charge us US$40 for a ride through the residential area to the old bull ring and back to Colonial area. He finally agreed to go for $20. We also thought that a bit expensive until someone told us gas costs about US$8 per gallon.
Some nice restaurants stop serving between 4 and 8 pm. Don't know if this is usual or because it was Sunday of a holiday weekend. Considering it's definitely a tourist town, we were surprised. But, there were plenty of other outdoor spots so no problem.
Coming back, we iscovered we needed the remainder of our ticket from the journey over - it was our Uruguayan visa which had to be turned in. This wasn't obvious to us as folks just kept tearing pieces off the ticket. Be sure to keep it!
The Uruguayans give a really bad rate on Argentine pesos, so if you are paying in other than Uruguayan pesos, suggest using dollars. We worked out the effective rate on Argentine pesos and it was about 5 to US$1. At that store we definitely paid in USD.
One other suggestion - wear comfortable shoes with good soles. Walking on the old stone streets and uneven sidewalks can be very uncomfortable and somewhat treacherous.
It was an enjoyable trip and we recommend it. Just keep in mind some of the points above and it will be even more enjoyable.