I take the A train from the northern tip of Manhattan to Brooklyn several times every week. Never seen anything problematic. It *is* very crowded, though.
I’ve been taking the A train from Far Rock for more than 25 years, and never had a problem. The trains run often, so it is a lot more convenient than the LIRR. It can be a little noisy when the schoolkids are traveling. The biggest surprise was when I chose to take the subway into Manhattan on a Sunday – most of the other passengers were family groups.