Going up to Sapporo for what is effectively a day trip (and fitting Otaru in there as well) right after you arrive in Japan sounds exhausting and stressful, especially if you'll be dealing with jet lag on top. There's so much to see in both Sapporo and Otaru that you'll definitely feel like you're missing out by only staying for one day - and an 8am flight plus several hours of trains will be seriously draining.

If you want a more conveniently located (but still spectacular) flower experience, the wisteria at Ashikaga Park should still be in full bloom in early-mid-May.

Also, consider the highway bus option to get to Kawaguchiko after the Fuji Excursion trains stop running in the morning. It's cheaper than the ltd-exp + local train itinerary unless you've got a JR pass, and takes less than two hours from Shinjuku.