Okay, I'm going to apply my knowledge on biology and taxonomy here. Ya'll are driving me crazy.
First of, dinosaurs as you're thinking were NOT lizards. They were indeed reptiles, but not lizards.
Snakes ARE lizards because they are in the same family, Squamata.
I WILL be counting (most) dragon-based Pokemon as lizards, since popular lore depicts them as similar. Some are more like lizards than others, but they will all be in a separate list anyway.
With that, here's what I see as accurate:
Onix / Steelix
Ekans / Arbok
Treeko / Grovyle / Sceptile
Snivy / Servine / Serperior
Scraggy / Scrafty
Helioptile / Heliolisk
Salandit / Salazzle
Sobble / Drizzile / Inteleon
Silicobra / Sandaconda
Dratini / Dragonair / Dragonite
Deino / Zweilous / Hydreigon
Janmo-o / Hakamo-o / Kommo-o
Applin / Flapple / Appletun
-All turtle Pokemon -- Again, yes a reptile, but not a lizard.
-All dinosaur Pokemon -- I already clarified why.
-All alligator and crocodile Pokemon -- While technically classified as lizards, they are, in fact, more closely related to birds, just like dinosaurs.
-Charmander -- It was based on a salamander, which is an amphibian not a lizard.
-Reshiram -- Fur = not a reptile.
-Toxel / Toxtricity -- Clearly salamanders.
-Dreepy / Drakloak / Dragapult -- They are Diplocaulus, an extinct genus of amphibians.
Now that just covers lizards. If we're talking about reptiles as a whole then we'd be here for a while.
If anybody has any questions, please ask me. I very much enjoy dropping knowledge bombs on people -- a good deal of you probably already know that.