What AC coupling capacitors value should you use for 100Base-FX (SFP)?

Using either 10 nF capacitors or 100 nF capacitors. My recommendation is to go with 10 nF unless you have a specific reason to use 10 nF caps. The argument to use lower value capacitors is to reject more lower-frequency common mode noise which might be overlaid on the high speed signal.

Note that many SFP modules already contain AC coupling capacitors.

X5R or X7R capacitors should be fine, you don’t need to use NP0/C0G for this.

Sources: Marvell 88E3015/88E3018 datasheet, section 6.2, figure 34: 10nF

Microchip application note, page 14 reference schematic: 100nF