I'd say Wing Commander 1 and 2 saw a warn out, but still very strong and resiliant Confederation. I was say they were their strongest up towards the Battle of Earth in which the fleet received a nasty blow.
Overall I'd say post-Wing Commander 2 up until the battle of the earth (bit before Wing Commander 3.
I'm not really sure when the confleet would have been the largest, but part of me wants to say the pre-war fleet, as confed had numerous battlewagons and several carriers, although most were lost in the first days of the war. During the war, there seem to be few times when confleet has a large amount of capships, possibly prior to the mid-2660s battles which gutted half of confleets carriers or in the post-2667-68 right before the armistice because confleet had finally gained an edge and was about to commission several new heavy carriers, and was also still creating CVEs which were proving their weight in gold.
I wouldn't call the WCP:SO Fleet the largest. Afterall, it took place about a few weeks after WCP. Now unless, ConFleet found a way to just create fleets of new cruisers and destroyers in a matter of weeks, or just pulled them out of their asses (take your pick), it would be safe to assume they were already in service - just not covered in WCP.
The most powerful fleet would be just before WCPSO, because lots of confed ships had their ass kicked by the bugs. Including a major fleet carrier (a supercarrier?).
The largest, in numbers, would probably be during the kilrathi war, where there was some major mobilization for the deacedes-long conflict. Maybe at the time confed was doing so well that the Kilrathi did that peace trick.