Places to stay near trainline from milan to lake como

there are two different lines, one to Como (the city) at the foot of Lake Como (which continues to Lugano and up into Switzerland) and the other which goes up the east side of the lake to the small town of Verenna-Esino midway up the lake (and the line continues up to Torino where it connects with the Bernina line up into Switzerland).

Do you know which line you'll want to be on?

What does "affordable" mean to you, and for how many people?

When are you looking to travel? Since the train time to either is so short, do you want it closer to Milan or your Lake Como destination? Any reason you can't go straight to your destination?

If you really want to stay between Milan and the lake (there is no real benefit in doing so), Monza is very convenient: it is where the line to Como and the line to Varenna diverge. It also happens to be a lovely, lively town with a beautiful park and former royal résidence.
I am not sure that it will be much cheaper than Milan, but you can have a look.

Initially I couldn't find much affordability near the lake for 2 people the end of March, but on further search, I've found quite a few under 200 for 3 nights. We had hoped to take the advice on Varenna, but not in our budget. We will just take the bus and visit. Any helpful transportation advice around the lake would be helpful. Buses,ferries as we'll be arriving by train from Milan.

At $200 for three nights, that's not much of a budget for Como. Personally, we stayed by the Lake in Como. We walked from the S Giovanni station to our hotel. We met people who did it as a day trip from Milan and it seemed very rushed and had to be orchestrated. If you plan to take ferries, factor in a lot of time. It's a big lake. While the slow ferries are very scenic, it takes a long time to go from one place to another. They are also not as frequent nor go as late in the evening as one might hope. In March, there will be even fewer ferries.

The 3 most famous towns in the mid lake area (which is the best area) and also the ones with most frequent ferry service are BELLAGIO, VARENNA, MENAGGIO. Bellagio is probably the most famous and most expensive, Varenna not far behind. Menaggio might be a little cheaper. The only problem is that March is low season, so some minor less expensive hotels may still be closed for the winter. Try Menaggio, or otherwise also Bellano, which is the next train stop north of Varenna.