This is a really interesting question and I’m looking forward to the answer!
In my very (very!) limited knowledge involving the accidents and incidents involving the CL-215/215-T/415 from Bombardier - which to me seems to be a more-or-less modern-day model of the Clipper given it’s amphibious nature (and one of my favourite planes!)- the majority of incidents/accidents seem to be due to mishandling the approach, controls or other operation during water scooping or water landing. Things like porpoising, striking the wing floats, failure in opening or closing water doors appropriately, or flipping over.
HOWEVER (and that’s a big however!) the CL-415 and its predecessors are fire-fighting aircraft, where rapid manoeuvrings and functionality on any available water source takes huge precedent over crew/passenger comfort, pilots are under much more stress and fatigue than commercial pilots, and most destination-to-destination landings are done conventionally, on land.
Still; waves, wind, smoke, pilot stress and other factors make it seem that landing on water is generally harder than landing on land. More importantly, perhaps, is that the passenger survivability on water is significantly reduced than it is on land - hypothermia and drowning don’t really occur on land, though fire is a greater risk.
Keep in mind that any weather that affects a land-based airport will also affect water surfaces in the area. A runway remains flat even in a blizzard. A lake does not, and so is that much more risky.
Again, I stress that I am as far from an expert as you can imagine, but knowing what I know about accidents, incidents and their causes (a hobby of mine), I feel pretty comfortable concluding that water landings are, on average, less safe than land-based ones.