Feraligatr, in both leagues, is second fiddle to Blastoise (Water gun is just that much better than both waterfall and bite). That said, if you don't have a Hydro Cannon Blastoise, Feraligatr is your next best option.
Feraligatr in great league should be rocking Waterfall (3.6[STAB] DPT + 2.67 EPT) over bite (4 DPT + 2 EPT), Hydro Cannon, and Ice Beam.
Feraligatr in Ultra League... has a different niche. Thanks to how dominant Giratina is in the Ultra league, bringing a Giratina 'gatr isn't a bad idea.
In this case, bite (6.4[Super Effective] DPT + 2EPT), Hydro Cannon (as the best generalist option) and Crunch are Feraligatr's best options. For the SPECIFIC purpose of countering Giratina, Feraligatr is THE BEST counter available in ultra league. Steelix may be better at specifically countering Giratina, but Feraligatr does so without suffering in neutral match-ups thanks to Hydro Cannon.
In master league (I know you didn't ask, but still) Feraligatr can't quite out TDO Kyogre. It DOES out DPS kyogre but that doesn't really matter in PVP.
In all three leagues, he pairs well with Metagross (who covers Gatr's weakness to electric and can generally out-neutral any grass type attackers not named Meganium, and has his weaknesses to ground/fire covered by Feraligatr) and charizard (who covers that grass weakness thoroughly and has his glaring weakness to rock covered by Feraligatr, as well as his weakness to electricity covered by Metagross)
TL;DR: Feraligatr is a decent option for Great/Ultra League. In Great, Feraligatr is largely the poor man's Blastoise (although the two are extremely close in performance) and in Ultra, he's the best Generalist/Giratina counter rolled into one, while again playing second fiddle to Blastoise as a water type generalist. Don't bother with 'gatr in master