Do you mean a flintlock pistol + flintlock rifle set, or two identical guns like a matched pair of dueling pistols?
I think most people probably match their own sets, i.e. they'll buy a flintlock 'kentucky' style rifle and then a 'kentucky' style pistol separately. I don't know of any retailers that sell matched pistol/rifle as a set. I have a .32 caliber 'Crockett' rifle (caplock) that may also exist in a flintlock version and Crockett-style pistols exist too. My Crockett is far and away my nicest gun and only set me back $300 used. Unfortunately I haven't shot mine yet but other people who own them are very impressed with the accuracy of .32 caliber rifles.
Gunbroker's a good place if you want to browse some guns, lots of inlines though so definitely search with keyword 'flintlock' in the rifle section. WTB ads in forum sales sections might also be fruitful; THR just got its own black powder sales section earlier this week.
I buy and sell black powder guns as part of my small business but I specialize in revolvers, my flintlock knowledge is relatively limited. I do have one and I enjoy shooting it when I can but it's a cheap Spanish gun, not reliable and not at all what I would recommend for a first flintlock unless you're a masochist, as it took some effort to get up and running after spending two decades hanging on someone's wall.
For a good first flintlock, you're probably going to want an American made gun. I think Pedersoli makes flintlocks too so that would also be a safe bet. Something manufactured in Spain or India may work well, it may not. Spanish guns are pretty 'entry level,' nothing wrong with them but my Spanish guns were cheap and it shows. Indian guns vary in quality; I attribute part of this to there being no Indian makers who are well known by name (Italians have Uberti, Pietta, Pedersoli, Spain has Jukar, India has ???) so there's less of a reputation to uphold, and also because Indian muzzleloaders cannot be proofed or tested in India. They are exported without touchholes because if they were functional they would be considered firearms by the Indian government and therefore illegal to export.
Good luck on your search for your first flintlocks!