There isn't a best fleet gear. It's all defendant on what you want to do with it. The Embassy Kits (Tier #3) are something to definitely look at though, they're awesome, at least the Engineering one is.
Based on the latest tribble notes, the best fleet weapons soon to be available this upcoming Thursday are Elite Fleet Disruptors [Acc]x2 [Dmg] with a proc that reduces shield resists -25% when it activates. The primary drawback -- they are T5 KDF-exclusive gear, so if you're a Fed, you won't have access to them.
Federation Elite Fleet Regenerative Phasers [Acc]x2 [Dmg] have an OK shield regen proc (been using the [Dmg]x2 [Acc] versions for a while on my fleet advanced escort), but I would prefer the KDF elite disruptors if I had access to them
Fleet Advanced weapons are also going to see an upgrade -- [Acc]x2 [Dmg]x2 will be introduced into T2 Starbases. These will be arguably among the best available weapons in game.
Regarding shields -- Elite Fleet Resilient Shields [Cap]x2 [Reg] [Adapt] are clear winners when you don't care for the 3-item set bonus ability. I usually replace my Reman set shields with these.
Shame I just picked up a full boat load of the current [dmg]x3[acc] ones...Do not suppose there will be an option to trade in for the superior option?
I've been asking for some kind of prototype refund option like that being given to Andorian phaser early buyers, but Cryptic has remained silent on the matter
I have full sets of Advanced and Elite weapons, so my losses will be considerable given how much was originally spent on the early [Dmg]x3 versions. This situation makes me wonder if Cryptic is trying to raise more short term revenue.