If you don't mind "cheating" with console commands you can use the fly option and use the pick underwater. As long as you don't change your vertical position fly won't put the pick away and if it does you can still take it back out while under water.

if it is deep enough to dig, the boat will always hit bottom there at least when the water is lower (if it varies at that spot) from any kind of wave action, and it will always float there when the water is high (assuming you dug it out as much as you could).

if you insist, after getting an area as deep as is possible, hoe-flatten to match is probably the way to go since that can be done from a goodly range.

the best advice I can give here is to not do it. Raise terrain (as a 'dock') or build a dock on out into the deeper water instead. You want a shallow flat area to park on and destroy the boat, and you want a deeper area to craft or park your boat, and those are distinct places. If its a channel to pass through, a little scraping won't hurt you, put a bench on the coast and repair as you pass through it. Not great answers, but its what I have to offer without mods or dev commands. I understand if its not what you wanted -- that can be frustrating for sure, but what you want may not even be possible and after hours of work, getting it 90% and living with it isnt a great answer either.

One thing I do sometimes: find a deep spot, put your boat there and board it. Now use the hoe to level the ground around to the level of this deep spot, it usually works better than digging, floating, digging, floating, etc.

Toss a cart in the water, and stand inside it; the cart floats, even though its top is below the waterline.

Wait until a storm, and watch the tide; the water goes up and down, which can allow you to get that last pickaxe hit you need to deepen your channel.