There *are* potential failure modes that cause a 1G ethernet link to negotiate down to 100M.
This could be a bad cable, as has been suggested, or it could be a bad connector on either the ONT or the WAN port of the router. More unusually it could be static or lightning damage (this has been observed)
As suggested: replace the cable first. Then try a different router for a while. If that shows the problem still then the ONT is suspect.
(No need for Cat6; Cat5e is perfectly fine, especially on such short links. But good quality, yes).
The ONT fault I had years ago (following lightning strike / surge and back feed etc) - nuked the ONT copper port in that it refused to negotiate above 100Mbps. It was evident very quickly as up and down just capped out predictably. Seemed reasonable at the time that the ONT had suffered like a lot of other kit we had that was either fried beyond recognition or just severely impaired by the strike / surge.
Doesn’t really sound like this is the OPs issue as this seems more variable throughput wise, up to full line rate - so ONT may have an issue, just not this particular issue.
If an ONT reset clears up the problem, then a fairly safe assumption is that the ONT is somehow faulty rather than cabling or router etc.