If you can get past the spaghetti manes,Funrise has the only official plushies of Derpy,Octavia,Vinyl Scratch,Cherilee,and Trixie.
Aurora makes ponies with better manes than Funrise,but they tend to have deformed heads
4DE makes the best official plush,but so far only Pinkie and Twilight are available(with Flutters coming soon).They recently announced Applejack(with a hat!) and Rarity.No Dashie yet,tho.
Build A Bear has all but AJ(she's coming soon though) and they are pretty good quality.
Ty makes Beanie ponies,with the just the mane six out so far.
Like everypony else said Amazon is a good choice.