If you only have three wires coming from the meter, and four going to the "main" panel. Then you're going to bond the neutral in the disconnect enclosure, so the direct answer to your question is all 3.
If there's a grounding bus bar in the enclosure, you'll terminate the grounding electrode conductor (the other end of which is attached to the grounding electrode) at the grounding bar. Otherwise, you'll just pull it into the box.
Next you'll bond the box itself, by connecting a conductor from the box to the grounding bar (or grounding electrode conductor, if there's no bus bar). This may be done already, depending on how the bus bar attaches to the box. If the bus bar is bonded via the attachment method, you're done with this step.
You're also going to bond the service neutral in this box. This will be done via a bonding jumper between the neutral bus bar and the grounding bus bar, or by connecting a conductor between the neutral bus bar and the grounding electrode conductor.
You'll connect the grounding conductor going to the "main" panel, to the grounding bus bar or the grounding electrode conductor.
When you're done the service neutral will be bonded, so it should be isolated from the grounding conductor everywhere else in the building.
You'll end up with something that looks like this.
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