"I am calling you(pl)"
Correct, since the -wa- object infix can mean "them" or "you" (plural), adding -eni at the end is the most common way Swahili uses to clarify which is meant (source: Wilson's Simplified Swahili, chapter 38). If you don't add -eni, then it is implied that you mean "them." And yes, the verb "to call" is kuita.
I would say "ninamuita" if I were to calling more than one person, for calling one person I would say "ninakuita". I don't know if this is a difference between Kenyan and Tanzanian Kiswahili. the -eni ending is usually used when you're giving the instructions to more than one person, at least in Kenyan Kiswahili.