Some EA-ish organisations are legally part of universities. For example, FHI is part of Oxford, and CHAI is part of UC Berkeley. In both cases when I donated to these organisations in the past it was legally a restricted donation to the university, to my recollection. I assume GPI is also part of Oxford.

(To be clear, I am not arguing that you should give to these two specific organisations).

The difference in effectiveness between even EA-aligned organizations may differ by a large factor, much larger than 3x. For instance:

• This 80,000 Hours survey found that a sample of EA leaders believe that the cost-effectiveness of donating to different EA Funds (representing different cause areas) may differ by up to 33x.
• GiveWell estimates that the cost effectiveness of their top charities may differ by up to 9x.

So I'd exercise caution before making donation decisions based on a 3x matching opportunity. You could end up donating to something that's much less than 1/3 effective.

(or specific program at a university)

How selective can you be here? As Khorton commented, this seems like it has the best chance of being worthwhile if you can restrict it a particularly high-impact program.

If you can only give it to a university unrestricted then I seriously doubt that taking your employer up on the 3:1 match would be the best use of the money.