I have been to Colonia more than 30 times and always take the one-hour Buquebus. You can buy your e-ticket in advance on their site and print a copy after paying for it with a credit card. They are always on time. Their new terminal at Puerto Madero near Retiro is easy to get to by bus and walking. Check in at 10:30 for the fast boat leaves Buenos Aires at 11:30. You have four hours to walk around, eat, do whatever, and then get back to the terminal around 4:30 for the 5:30 departure. I go to the park on the main street where I read a book.
ColoniaExpress has been in business only two years. I tried once to buy a ticket through their website, but it wouldn't allow me to purchase a return trip on the same day. That, in addition to the location of the boat in La Boca, is reason enough to continue going by Buquebus. Colonia is not worth seeing any longer than a few hours, since you get to go every six months.
Buquebus fare hasn't been increased from what it was ten years ago. It's tied to the dollar and has always been $70.
My visa expires July 18, so I'm going this week to Migraciones for an extension.