Once a woman’s pregnancy has been confirmed, is it okay for her to have relations with her husband? (as she is no longer having a menstrual period, she is presumably no longer in niddah?).

Shalom U'verachah, If she is pregnant there are opinions that she is allowed to have relations presuming of course that she went to the mikvah after her last bleeding and she does not see bleeding. There are opinions that she still has to observe the 60th and 90th day since her last period and not to have relations on these days and to check herself. Kol Tuv