EZE can have very long lines for immigration and customs; most of the time, they X-ray every incoming bag. I don't know whether you can avoid this if you're connecting to Uruguay.

You'd be going from EZE into the city at rush hour for the BuqueBus, which has good discounts for advanced purchase tickets, but I've been told that the faster boats (hydrofoils) to Colonia can sell out on weekends. In principle, you're required to check in for these boats at least one hour in advance, as you must do border formalities with both countries before boarding.

It's a somewhat interesting trip by water, at least with the hydrofoils, to Colonia which is itself worth a visit of a day or so. I'd suggest staying one night in order to see the historic city and port at night as well as during the daytime. IIRC there's a museum near the BuqueBus terminal and another museum of contemporary local art near the old port. We walked throughout. IIRC there's a Sheraton (just beyond the old downtown and port) which is pretty inexpensive plus some small local hotels in historic buildings in the center. Try some local wines with lunch and dinner, which is similar to Buenos Aires restaurants with lots of dead cow but cheaper.

AR flights are notorious for cancellations, delays, and schedule changes, but they're DL's SkyTeam partner here.

Note that if you try to book the AF (or some other) flight for the next day, there aren't good and interesting places to stay near EZE. You almost need to go into the city for the night, which itself is fun and interesting. Given that, you might want to check whether the much closer domestic airport AEP has flights to MVD. I don't know whether it's strictly 100% domestic or not, but don't expect many facilities there.

The short haul AR flights seem to have good award availability using DL miles, although you might need to call DL to book these. They can be relatively inexpensive but note that you cannot use the cheap fares for local residents. [They check your documents for this; there's a thread on it in the Argentina destination forum.] An advantage of using DL miles is that you can easily book the ticket with DL and use a USA credit card without any hassles. I called AR to check that everything was booked correctly and to get my seat assignments. Of course the AF flight is likely to be more comfortable if you can use it.