I haven't spent enough time in the city of Como to have an informed opinion about it. I know it has some museums and is convenient by train. However, most folks go to Lake Como to see the very picturesque small towns along the lake, not for the city environment of Como itself. The mid-lake area is considered the most picturesque part of the lake, and it's some distance from the city of Como. The most convenient places to stay for exploration of the lake are the towns with ferry service in the mid-lake area. The ones most often mentioned are Varenna (population under 500, not cheap), Bellagio (population 2500, not cheap), Menaggio (population 3000, probably a bit less expensive). There are other options, but those towns are most convenient for zipping back and forth across the lake. Varenna, on the eastern side of the lake, is the only one of the three with train service and is thus the easiest to get to from the city of Como. The others can be reached by bus or ferry from Como.
There is a lot of demand for lodging in the mid-lake area, and rates are not low; I would expect Como to be less expensive but would consider it a less-desirable location for enjoying the lakeside atmosphere. It doesn't help that the US dollar has weakened a good bit in the last year. You might check booking.com to see what is currently available. I find the reviews on that website generally accurate; you can't leave a review there if you haven't actually stayed at the property. When you've found one or more possibilities, go to their websites, where you may find lower rates than on booking.com.
Although June is not quite as busy as July and August, the fact is that occupancy rates that month will probably be very high, and all those folks will be sightseeing around the lake. Bellagio is usually the most crowded destination. You should not expect a peaceful atmosphere, at least during day-tripping hours; if you stay in Como, you'll be among the day trippers. I had no problem getting on ferries between August 30 and September 2, 2024, but others have reported such long ticket lines that they made a point of going to the ferry dock early in the morning to buy a day-ticket to use later in the day.
As for whether Lake Como is a practical destination to slot between Como and Geneva, well, I think it's iffy. The Colmar-Geneva trip can be made in less than 5 hours. Colmar-Como-Geneva would be more like 10 hours--plus about 2 additional hours if you stayed in one of the mid-lake towns instead of Como. Including Como necessarily means a lot of $$$ mileage on Swiss trains unless you are confident enough of your planning to buy Saver Day Passes soon after they go on sale.
Perhaps others can suggest alternative scenic towns that are more geographically convenient in this situation.
