Please give advice on itinerary

My husband, my almost 5 yo son and I will go to Japan (May30-June16). We had gone to Japan couple times but never went north. Would like advice on our itinerary. No driving. JR only.

Day1-Arriving at Narita after 11 hours flight. Will stay at an airport hotel to rest.

Day2-From Narita to Nyuto. I believe it will take 4 hours of JR and 50 mins of bus. Is that a bit too much traveling on one day?

Day3-Nyuto onsen-would like to stay one more day to enjoy onsen. Any good suggestion on day trip nearby?

Day4-5-Sendai; will visit Matsushima. Is this enough time? Any other suggestions in Sendai?

Day6-Hakodate-we know it will be more than 5 hours travel.
Will stay at a pension and enjoy dinner there. Likely will not do too much today.

Day7-Hakodate-morning market;
Motomachi area? Shopping?

Day8-Day trip to Yunokawa onsen. Does it worth a day trip? To Mount Hakodate in the evening.

Day9-To Noboribetsu.
Day10-Noboribetsu-day trip to
Toya

Day11-Sapporo
Day12-Sapporo-day trip to Otaru
Dat13-Sapporo-day trip to Furano-any flowers to view yet?
We don't want to haul the luggage to Furano and our only interest is to Tomia farm.

Day14-Not sure what to do today. Will check out from the hotel and wait to catch the night train to Tokyo. Any suggestions? Sapporo beer factory?

Day15-Tokyo
Day16-Tokyo

Day17-Back to US

Please give your suggestions. Thank you!

Day2-From Narita to Nyuto. I believe it will take 4 hours of JR and 50 mins of bus. Is that a bit too much traveling on one day?

I guess it depends on the person. It would be no problem for me.

Day3-Nyuto onsen-would like to stay one more day to enjoy onsen. Any good suggestion on day trip nearby?

Lake Tazawa and Kakunodate.

Day4-5-Sendai; will visit Matsushima. Is this enough time? Any other suggestions in Sendai?

Yes, a full day is enough!

Day6-Hakodate-we know it will be more than 5 hours travel.

The following order makes better sense in terms of geography: Narita - Tokyo - Matsushima - Nyuto - Hakodate!

Day8-Day trip to Yunokawa onsen. Does it worth a day trip?

Yunokawa is INSIDE the city of Hakodate! You don't need a full day to visit Yunokawa. If you have time, I recommend to visit Onuma Park:
http://www.japan-guide.com/e/e5356.html

Day9-To Noboribetsu.
Day10-Noboribetsu-day trip to
Toya

Toya is west of Noboribetsu. It makes better sense to visit Toya on your way from Hakodate to Noboribetsu, although, I understand there might be a luggage issue.

Furano-any flowers to view yet?

Yes, there should be some flowers. But it is too early for the lavender.

Day14-Not sure what to do today. Will check out from the hotel and wait to catch the night train to Tokyo. Any suggestions? Sapporo beer factory?

Some suggestions:
http://www.japan-guide.com/e/e2163.html

Thanks for your advice. we wil make some changes on the plan.

I recently put some pictures of Nyutou onsen up on my blog: http://hoshisato-travel.blogspot.com/2007/07/japanese-secret-onsen-1-nyutou-onsen.html
It is my favourite onsen because it look still so very traditional and genuinely Japanese. Click through on the pictures to get a better overview.

I've added Yunohira Onsen (湯平温泉) on Kyushu to my list of favourite onsen: http://hoshisato-travel.blogspot.com/search/label/onsen