What is the best way to get from buenos aires to punta del este? should we go to colonia on the way, or make it a day trip from buenos aires?

Your question is not clear for me.

The best way to go to Punta del Este from BA is, obviously, by plane.

Best way if by plane. There are several daily flights.
If not, you can take the Buquebus, and there are two options one takes you to Colonia and from there bus to Punta. The bus is waiting at the Port.
The second option is a Buquebus to Montevideo, and again a bus to Punta del Este.
From Colonia to Montevideo it is aprox 180 kms, from Montevideo to Punta it is aprox.140 kms.
Problem is that buses, I believe do not exceed 90 kms./hour. This is why flying is much better, it is a short fly. Of course a last option could be flying to Montevideo, and taking the bus from the airport to Punta.

and just to give a sense of timing - by plane PdE is probably an hour or less. By buquebus, combining the ferry and the bus, you're looking at 5-6 hours of travel time.