In the U.S., can a Student Pilot (Airplane-SEL) while training with an instructor and being the "sole manipulator of the flight controls," credit 3 takeoffs and landings to a full stop in accordance with 61.109 (a)(2)(ii), all completed between 1 hour after sunset and 1 hour before sunrise, towards meeting the night takeoff and landing experience (to carry passengers) specified in 61.57 (b)(1)(i) and (ii), as long as they were completed within 90 days of carrying the passengers and the pilot now has a PPL (Airplane-SEL)?
Yes, with the caveat that the flight is in the same category and class. Recent experience isn’t invalidated by the change in certificate. 61.57 (b) has two requirements listed in sub paragraphs:
(i) That person acted as sole manipulator of the flight controls; and
(ii) The required takeoffs and landings were performed in an aircraft of the same category, class, and type (if a type rating is required).
You have met the first. The presence of the instructor and the fact you are a student pilot are not relevant. The second is more than likely true unless you got your MEL certificate at or shortly after your PPSEL. In that case you could be night current in a single engine aircraft but not a twin (or the reverse if you got your private pilot in a twin and added SEL afterwards - not very common but possible.)