Is it acceptable to mark off or comment on someone's presentation based on their non-standard English accent? I am working as a TA for a seminar course and class presentations are considered a significant part of the total mark for the course.

Some of the students in the class — who mostly happen to be international students — do not perform the best presentation in terms of the communications of ideas with the audience.

It is mostly because of their thick accent and other flaws in their English, making the presentation hard to understand for the audiences.

What is the best marking strategies in these situations?

I am skeptical about commenting on this issue and discussing the problem with the students or reducing a part of the mark for the lack of communication quality, as I am afraid it would come across as racist.

The university is in North America and about 80% of the students are native speakers of English.
There are two ways to interpret the issue that is being raised. One is that the people simply have accents and not completely correct grammar in spoken English... but not to the point that it seriously impedes intelligibility. The other is that their English is so poor that it does greatly impede intelligibility.

The former is of little consequence, of course. The latter is a serious problem, in fact. It's not about bias for/against languages/nationalities, but about the context in which one operates. If one cannot communicate effectively, that's a minus. Even if/when people are "understanding", it's still not a plus, but a minus. Overcoming such an impediment should have a pretty high priority... as opposed to simply believing that such an issue solves itself in time. In particular, this will not happen for people whose English is sufficiently compromised that they spend nearly all waking hours with their fellow speakers, and thereby never practice the local language (as Dir. of Grad. Studies in Math. at my university on two different occasions, and participating in such issues for 35+ years, I've seen many cases).

In particular, outside of super-special cases, it serves no grad student well to have English be an obstacle. It will significantly obstruct their hiring on teaching-communication grounds, if nothing else. And, unavoidably, it reduces the impact of their portrayal of their research work.