What are the best schematics in the game (and where do I get them)?

There is an excellent, if somewhat lengthy, discussion of crafting optimization here. Well worth a thorough read.

The upshot is you have to consider the available crafting materials and slot distribution of schematics. Collectively, I call all that the "slot economy," because some of the trade-offs are zero-sum. When you pick something to optimize, like say increased probability of making critical hits, something else has to give.

Fortunately, most of the best schematics are actually pretty close. It's not like one is 10x better than the next one. You listed most of the best, but fwiw, here are my preferences:

1H: Axe of Green Edges

2H: Chromatic Greatsword

Staff: Encore, Wrath of Lovias

Dagger: Hakkon's Mercy, Coiled Strike

Bow: Hakkon's Wrath, Grunsmann's, Elgar'nan Enaste

Armor: Superior Prowler Armor (for all classes)

But really, all the list above tells you is that my crafting bias is towards crit/crit damage and upgradeability. If you have a different bias, like towards attack or flanking damage, you'll get a different list.

I usually like to go with attack for warriors and mages and ofc I go with dex stuff for rogues.

Next question is what helmets?

Also, what upgrades are good? I admit I don't have as many of them so need to know where to find them. Where do I find the schematics you listed?

Maybe I made a bad assumption? I assumed you already had most of the schematics available through the Golden Nug. If that is not the case and you have to farm all schematics from scratch, I can give you a more accessible list. As capn noted, most of my favorites are DLC only.

The Superior Prowler Armor vs the Mail you have the difference is basically a little more offense from the former vs more defense from the latter as the important difference is 4 leather utility in the armor that is replaced by 5 leather defense in the mail.

If you do want to "farm" the Canyon Merchant for it, then you need to get the Short List perk from Connections first, then the most reliable trick seems to be to save in a zone that isn't Hissing Wastes, then go there and see what the store has listed. If it has the schematic, buy it, if not then exit the game and then reload the save in the other zone. I think finishing a plot mission also resets the stores, but I am not sure what else is really supposed to do it.

For just run of the mill tier 3 stuff, Cradle of Sulevin has a lot of chests that can drop tier 3 (leave at least one item in a chest and it will respawn items when you return). Valeska's Watch in Emprise also has a fair amount of them.