With the way the new rules of the phantom uncloaking before anyone moves, can I put an intelligence agent in the crew slot so I can look at what a ship is doing before I uncloak? Or, do I have to uncloak and then use my intelligence agent?

YES - Decloaking occurs AFTER players have resolved all other abilities that trigger at the start of the Activation phase - so you can take a peek and then decide which way to go.

This would include resolving the following crew cards before the decloak:

"At the start of the Activation phase, after players have resolved all other abilities that trigger at the start of the Activation phase,"

So yes, Intelligence agent happens befor decloacking.

[edit - ]

Awesome, thanks for that.

Yeah and don't forget if you are at Range 3, you can uncloak, move into range 2 and then use your agent now that you are in range to use it as well.

Lots of options available.

Yeah and don't forget if you are at Range 3, you can uncloak, move into range 2 and then use your agent now that you are in range to use it as well.

Lots of options available.

No, you can't. The decloak explicitly happens after everything else--including Intelligence Agent--has been resolved.