Lake Toya or Lake Shikotsu?

Hi
Im trying to decide which lake to visit: Lake Toya or Lake Shikotsu. Will arrive by train from Asahikawa around 14.00-15.00hrs and depart next day around 15.00 hrs. Is this enough time? Or is it suggested to stay another night, if so what is the best itinerray? Would appreciate any views and suggestions, many thanks in advance.

Lake Toya has lots of onsen ryokan (hot spring hotels) of all sizes, and a volcano nearby that is accessible by ropeway. Lake Toya is relatively easily accessible by public transportation:
http://www.japan-guide.com/e/e6725.html

Lake Shikotsu is much less developed. There is only a small village with a small number of lodging to select from. There are some nice hiking trails, but it is recommended to have a car:
http://www.japan-guide.com/e/e6736.html

It also depends on the rest of your itinerary.

Ok great, I think we will visit Lake Toya.
Our itinerary in Hokkaido will look like as below. Kindly let me know if it seems ok? It is for the end of September and we will be using our railpasses.

Day 1. Arrive Sapporo New Chitose Apt. Go to Hotel in Sapporo (Hotel TBA)

Day 2. Go to Sounkyo Onsen, arrive around midday. Stay 1 night (Hotel TBA)

Day 3. Go to Lake Toya. Stay 1 night. (Hotel TBA)

Day 4. Lake Toya until 15.00ish. Catch train to Hakodate. Stay 1 night (Hotal TBA)

Day 5. Morning market Hakodate. Then early train to Sendai....

It is a fast paced itinerary, and you will spend a lot of time on board of trains and buses. Have you thought of flying into Asahikawa Airport instead Sapporo? You might be able to save a few hours by doing so.

Also, the current itinerary won't let you see much of Hakodate.

Thanks Uji for your reply.
We are already booked to fly into Sapporo and cannot change ticket. I agree it is a fast pace itinerary. We will be moving onto Sendai region, Japan Alps, Kanazawa and Kyoto within 2 weeks...
If we add an extra day at Hokkaido, where would you suggest it would be? Not too interested in Hakodate, mainly to see the lights from the mountain and fishmarket...
Thanks again.

f we add an extra day at Hokkaido, where would you suggest it would be?

It depends on your interests. You could add time in Sapporo/Otaru (nice cities). Or Furano/Biei (nice countryside) or Daisetsuzan National Park (hiking).