If there isn't a car, then getting a train pass an essential. Naturally, going by tour is convenient as the train system in Hokkaido isn't as fabulous as the Tokyo-Hiroshima route.
But if there isn't that option, then use the train. Buses aren't bad either as there are highways, but finding out the schedules for buses... I don't know where such information is available.
With regards to shopping, it depends on what you like to buy. Sapporo as compared to Tokyo has less options. But as the name Sapporo goes, Sapporo beer and other beverages are cheaper then at Tokyo. Similarly, Kirin beer enjoys a cheaper price. Many famous chocolate factories are in the vicinity of Sapporo. The issue is that the prices are usually fixed no matter which part of Japan you are in. It is just the variety is way more at the factories.
Getting to the choc/beer/cheese factories... Use Japan Guide. I recommend train to the nearest station followed by a taxi. Or just a taxi from the hotel. Taxis in Hokkaido are generally more reasonable as compared to other parts of Japan.
For usual apparel and other shopping, going along Sapporo Dori is fine. The department stores are between the Dori and the Sapporo Station.
Going to Otaru= Train
Please buy a hokkaido train pass
I have no idea how big your bags are or how big the lockers are.
They do have lockers of various sizes.
Otaru via JR HAKODATE LINE all the way till Niseko station. One train, no transfers
I would presume that there are trainers, a quick google search gave me
http://instructortrainingacademy.comUse agoda or some other hotel website for hotel booking.
Niseko via JR Hakodate line to OSHAMAMBE then via JR Muroran Line to Toya
Take a Donan bus from the Toya station to Lake Toya.
Cycling or walking. There is a boat ride around the lake too. Up to your pretence. The cycle will take no more then an hour.
Again... it is the train... From Toya station to Noboribetsu station. From noboribestu station take a bus or a taxi to the onsen. If you made prior contact with the hotel, call them now, and they may send a minivan you way.
Trek etc. Ask hotel for help. They would provide you with a map or point you to the nearest tourist info counter more a map.
Kuttaro is about 45 min according to Google maps. It is north of the town. The lake is nearly a perfect circle making it nice to look at. There may be mist in the morning. Think San Fran.
To stroll the length of the town takes about half an hour. So it is pretty hard to get lost. The central part of town can be covered in 20 minutes.
Nanoe
Train please. Make use of your train pass
Hakodate mountain travel info
http://www.japan-guide.com/e/e5354.htmlWalk to the market
Use a map provided by hotel or a tourist info counter. Or just google it.
Western area info
Walkable
http://www.japan-guide.com/e/e5351.htmlFor shopping. Along the bay. The brick warehouses are popular. Especially the cheesecake. Just ask random people "Red Brick Warehouse"
The Western area has stuff too to buy. Window shopping.
In Hakodate airport there are many snack shops. Jagabee; Ishidaya; Rottakei... etc