Best bike tour stops in Wachau Valley

Here's what I'd suggest -

Take the south bank of the Danube
Visit Aggstein Castle (big hike up the hill, but worth it)
Take the ferry across to the north bank at Spitz (check the schedules, etc.)
Check out Spitz, Weissenkirchen, stopping for lunch at a Weingut (so much more than just wine) along the road.

Head towards Duernstein, stop and climb to the destroyed fortress where Richard Lionheart was held for a fantastic view, buy some apricot things
Have a drink at the Altes Presshaus in Duernstein.
Carry on to the Krems train station.

I rode a bike from Melk to Krems after seeing the Melk Abbey with its amazing library and gardens above the town.
There's a dedicated flat bike trail running through the Wachau Valley toward the medieval town of Krems.
The bike trail on the southern bank of the Danube takes you past vineyards and crumbling castles.
The historic town of Durnstein with its ruined castle, where King Richard the Lion Heart of England was held captive,
can be visited by crossing over the Danube on a frequent 10-minute ferry. When you arrive at Krems the medieval city center is fascinating. From Krems you can take the train
back to Vienna. There are a few bike rental outfits that will let you pick up a bike in Melk and drop it off in Krems and vice
versa. It makes for a fantastic daytrip!

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Sounds like a great trip.

Any recommendations on where to rent bikes in Melk? We plan to take the train from Vienna to Melk and then bike to Krems. Thanks!

If you want to combine a train ride with renting a bike, here you are:
https://www.oebb.at/en/reiseplanung-services/am-bahnhof/nextbike

But you can hire bikes independently as well:
https://www.nextbike.at/en/niederoesterreich/

You can pick up your bikes in Melk, ride to Krems, and drop them there.