If Gyarados is trained as you've described, and also has 31/31 IVs in every stat (key point!), then its stats should appear as follows: 115 HP, 129 Atk, 67 Def, 48 SpA, 81 SpD, 89 Spe. As you would see, your HP and Defence are higher than expected, and the others average about six or seven points below. This is not nearly as drastic as you make it out to be, and would easily be explained by deficient IVs and mistakes recording EVs.
You said you 'bred' Gyarados: that's good, but did you breed it specifically to get 31/31 IVs on every stat? If you didn't, you will never achieve the optimal stats outlined above. Further variance in the stats would also be explained if you have recorded your EVs incorrectly. As KRLW890 suggests, you should use Pomeg, Hondew, Grepa and Qualot berries to clear EVs on the stats that you didn't train much, and note if the berries take effect, i.e. do not display 'Its stats won't go any lower!' If they don't display that message following use, then you have indeed made errors. Keep using berries until they do show the message.
If this wasn't obvious, there is no particular point where you will 'gain the boost' from EVs. Your Gyarados is already gaining the boost. The amount of points you gain from EVs scales linearly to your Pokemon's level: don't expect to see +63 points at level 33 like you would at level 100.
