Amiami, goodsmile, and amazon!
Lol. Fakku. I bought a "hen-tie" shirt from their dealers room booth at otakon a few year back. They're pretty chill. B)
Amazon or eBay
Amiami is my go to site cause their ain't any bootlegs there. CDJapan, cheap anime magazines compared to other sites. AliExpress, not the best place for actual official anime merch but if you don't mind getting cheap pins, shirts, posters, or keychains then it's a good place
Amiami is where I go to pre-order figures and other merch. I mainly use Solaris Japan, and Nippon-Yasan for second-hand figures. I might rarely buy stuff from Amazon JP, or Ebay but those are more of a last resort.
I usually go through AmiAmi and HobbyLink Japan, but I've found the deals on Tokyo Otaku Mode to be pretty good, though you do have to wait an extra month or so to get the figures due to international release dates being later. Nippon Yasan I use for Bandai Premium Web items like S.H.Figuarts.
Play-asia, Goodsmile and Mandarake are pretty good. Mandarake is pretty nice as far as aftermarket sellers go because they're pretty anal about authenticity, so you likely won't find any knock-offs there. Also Amazon is good so long as you're careful about who you buy from (again, risk of knock-offs).