Max DPS vs. Max CP

I dare say that the answer is..97% of the time, max CP.

You must know that those pokemon that has higher max CP are mostly stronger than those with lower max CP. why?

Easy, for example when your cloyster reaches a lv.40 it's maximum CP is only a mere 2052 while Lapras will have a staggering number of 2980. The difference is too big, it's too clear, cloyster is not Lapras' match at all. Even if cloyster has better moves than lapras, the number is just too different.

However, there are times when the higher DPS might make you consider. ( maybe not now but in the future when more pokemons will be introduced ). However, this can only occur when the CP of both pokemons are not too far away, since there are no pokemon currently who's moves may make you consider in the higher CP levels, I will just use the closest example in arcanine and flareon.

Arcanine's max CP is 2983 and Flareon has a max CP of 2643. Arcanine's Fire type primary move is a Fire Fang with a DPS of 8.33 [ not counting STAB ] while Flareon's primary move is Ember with a DPS of 9.52 [ not counting STAB ] with both of them are able to learn Flamethrower as a charge move. Now, Flareon has a better fire typing move than Arcanine but there is still a considerable difference of 340 CP points. Hence, the conclusion is Arcanine is a better choice ( probably, since I can't calculate that, but I'm 99% sure ). But if, in the future, a fire type pokemon with a max CP of 2900 and has an access to ember is introduced, it could be giving Arcanine a run for their money.

P.S btw, I don't know why Cloyster is ranked as the best for ice type since Lapras can learn both of Cloyster's highest DPS move and with a STAB too. Basically Lapras is just an upgrade for Cloyster.

The Haunter-Gengar example was likely wrong.

Secondly, the dps of a move is different from the dps of a move on a pokemon (which is different from total damage output, but I'm getting ahead of myself).

This site, correctly or not, prioritizes "damage per second"--how much damage a move does divided by its cooldown time. First off, in reality, this may not always pan out for different offensive styles. If you don't care to dodge, it may generally pan out, but, if you do care about dodging, then a slight difference in cooldown between two different moves may not be enough for you to fire off one+ of the faster move and still frequently enough dodge.

That said, the "dps" of a move as measured on this site is not a useless metric. It can determine whether Fire Blast or Heat Wave is better on Flareon, and it's even more important whether or not certain fast moves are good, useful, terrible, slow, etc.

Now, "damage per second" is of course different from "total damage": supposing that "total damage output" can reliably be scheduled according to damage per second, you still need to know how long your pokemon can last in battle, the "seconds" in which it is dealing out damage per second. Because "CP" is an aggregate stat that factors in the damage stat (dps independent of consideration of moves) and the defense and stamina/HP stats (longevity independent of consideration of moves), it can be viewed as a stat that roughly tells you total damage output of a pokemon in a battle (again, independent of consideration of moves).

If A Cloyster has higher attack than A Lapras with the same moves, it will do more damage over a common period if they always do the same moves at the same time with the same effectiveness. Lapras could last longer or shorter in the battle, depending on different effectiveness and if Cloyster gets critical knockouts quicker.