Hakodate has aesthetic cityscape as you'll recognize from various vantage points up along the slopes of Hakodate Mtn (one that ropeway goes to), offers unique visuals with trolley cars and some interesting architecture, and of course has the morning seafood market which is its number 1 attraction. Onuma is a picturesque national park area worth checking out and that's nearby.
Having said all of this, there's not a whole lot to see/do there and it is not a big town like Sapporo with tons of shopping and food. So I think you might find 4 nights in Hakodate to be a bit much. If you're more about sightseeing, then I think a couple days would be sufficient for Hakodate. But if you're content to just chill out and enjoy a much cooler weather than Tokyo or Osaka, Hakodate would be good.
The seafood market mostly closes down in early afternoon, I believe, and then the area around Hakodate Station really would not have much going on. There at least used to be a department store a couple blocks away, but that one went out of business. The area near Goryokaku where the trolley takes a turn is more happening.
Nonetheless I would recommend you still stay near Hakodate Station, as it's close to the station, market, walkable to the bay area complex, and many bus lines depart from there.
Yunokawa Onsen would be Hakodate's onsen, and there are some onsen hotels that face the ocean. But I will tell you that the whole area is sort of a non-descript residential area and the seaside lodging would likely be sitting on a busy highway. It is not like Hakone or Kusatsu. Nonetheless, if it's me, give me any onsen with a view and I know I would enjoy it.
With the virus in the mix, I don't know how the morning market is like. It probably is nothing like what it's always been.
If the Olympics do indeed occur, I would expect the takuhai service (luggage forwarding) to be even slower than usual. You should not count on 2-day delivery from Tokyo to Hokkaido. I feel like the service is becoming slower with less and less guarantees during peak periods. I think it's because of more tourists (pre-Covid) and Amazon Prime and all that. 10 years ago, the expectation was same-day delivery from Narita to greater Tokyo as long as it was like early afternoon or earlier. These days during peak periods they won't guarantee anything, not even next-day delivery from NRT to Tokyo. Shipping from Saitama to NRT, they advise shipping at least 3 days in advance during peak period. So who knows about Hokkaido. And Olympics would definitely be a peak period.