Firstly, I'm speaking about Canadian coins only, based on my observations.
I find Charlton's is a pretty good guide for variations, and less so for pricing.
J&M's and CoinsandCanada's online catalogues are useful for pricing, though they skip a lot of variations (moreso J&M than CandC).
It seems like with some vendors there is room for negotiation on price, and others hardly none. Like most small businesses, I suppose it depends on the individual who owns the business.
ebay prices should be lower than buying from a store or collector in person, IMO, as you never have the coin in hand before pulling the trigger to purchase - mostly it works out, sometimes not. The odd bent coin would be an example of a coin that looked great in pics, and where the seller never said anything about the bending of it. Even ICCS graded coins that are allowed to go to auction rather than BIN often sell for far less than Charlton's or J&M's posted prices.
ebay offerings that are BIN's with Best Offer options are often way over-graded, in my experience.
Generally, it looks to be a tough market to move high value coins in particular, if your aim is to get near published prices. My definition of high value for the purposes of this post would be around $500 or more.