Short answer:Yes, please.

Long answer:
I don't let just anyone have access to my cock. So, in a way, by allowing a woman to have intimacy with me I'm paying her a complement. A complement in return is appreciated. Likewise, a woman is extending a complement towards me by letting me have fun with her body, and I know she'll like it if I show my appreciation by saying something nice. If I say nothing about those parts that she normally keeps private and just get on with the sex, she could easily wonder if her, tits, pussy, butt, are to my liking, or not.

It's always better if any comment is complementary. So, even if you've had bigger cocks, you can still say "Oh that's a nice big hard-on". It's just a matter of being tactful and generous. 'Nice little stiffy' might spring to mind when you clap eyes on it, but you're going to get a better performance from the guy if you seem to be impressed. So it's in your interest to say something nice.

Now, if the guy pumps you for your honest opinion, ie. "have you had bigger? etc. then you have to be honest. And if you have had bigger, you just have to hope that he's not going to be crushed by hearing it. However you can't take all the responsibility for protecting him from feeling crushed. Guys have to learn to keep their own self esteen together. But you can do a lot to help, or you can do a lot to make it difficult for him. It's your choice.