Where to Find and Catch Manaphy
From Pokemon Go Wiki
Manaphy are found and captured in Nest and Habitat locations.
Nests
Manaphy Nests are locations that consistently spawn Manaphy.
Habitats
Manaphy Habitats are spawn locations where Manaphy is likely to be encountered, but not guaranteed the way a Nest is.
Additional Tips and Information
Best Nests
If you know a really good nest or any of the nests above is really good, list them here: