The answer, like most places, depends on what kind of things you are interested in and whether you want to visit the surrounding areas too.
Things I found interesting in/near Bogota:
- The gold museum
- The Botero museum
- The salt-mine cathedreal of Zipaquirá (1-2 hours drive away, depending on where in Bogota you are and the traffic)
- The Monserrate Sanctuary (on the hill above La Candelaria, there is a teleferico if you don't want to walk)
- Walk around looking at the street art (there are tours for this too)
- Find somewhere to play Tejo - throwing rocks at gunpowder triangles on a clay board, while drinking beer
- The La Perseverancia market, especially the food stalls on the second floor
- If you like beer, go to the Botoga Brewing Co
- The Police History Museum has many things, but a bunch on the drug cartels (and their influence on the civil war). Obviously from the government's side of it
The salt cathedral will take most of a day, the rest you can do a couple in one day.
Bogota to Medellin is an hour flight, plus the time at the airport, 30-60 mins getting to/from there, delays etc. An alternative is a 9 hour bus. Another alternative is going to the coffee triangle and the Corora valley (unique wax palms) on the way for a few days. Bogota - Salento - Medellin is a 6.5 hour bus for the first part, 5.5 for the second.
Things I found interesting in/near Medellin:
- Catch the metro then the teleferico to go visit Parque Arvi up the hill.
- Eat Bandeja Paisa, and then try not to fall asleep in a food coma
- Watch Atletico Nacional play a game of soccer. By chance we were in Medellin when they were playing the final of Copa Libertadores at home, the city was a bit crazy that night.
- Learning more about the history of the cartels and their influence on the civil war. There are plenty of tours that cover the history, with greatly varying approaches - the one we went on had guides who said that all parties (cartels, government, guerillas, paramilitaries) did horrible things, we heard of other that basically glorifies Pablo Escobar.
- Visit Guatape (2 hour drive away), and climb up La Piedra de Peñol for a view over the country side
Were the other things before you go to BA in February, after you return from the boat, or not sure? Jan/Feb is the rainier season for the Salar. Also, did you have a specific route getting to South America? e.g. via SCL, or via LAX and starting it in Colombia?
With the Salar de Uyuni, you can do a small round-trip from Uyuni, or a three and a half day crossing of the Atacama desert from San Pedro de Atacama (northern Chile). If you were going via SCL, there is the option of flying to CJC, seeing San Pedro, doing the crossing, and ending up in Uyuni - you may not have the time or inclination for that though.
San Pedo de Atacama is a tiny town, near to the valley of the moon, which has no life at all. If you like stars, there is great stargazing there. You used to be able to visit the Atacama Large Milimeter Array too, but not at the moment.
For acclimatisation to the altitude, it depends on where you are coming from. La Paz, Uyuni and the Salar are all around ~3600m, Sucre 2750, Bogota 2600, San Pedro de Atacama 2400 and Medellin 1500. If Colombia was immediately before Bolivia, you could potentially do Medellin first before Bogota and then fly to La Paz, as Bogota it's not significantly lower than Sucre.
If you need to get from La Paz to Buenos Aires, I think the main option is Latam via LIM. Bolivia de Aviacion is an option too, but I don't know anyone who has flown them.
