What’s the difference between polyatomic compounds and polyatomic ionic compounds?

Any compound with more than one atom is a polyatomic compound. Any ionic compound with more than one atom is a polyatomic ionic compound.
For example, a monatomic compound would be helium, with a formula of He. A polyatomic covalent compound would be something like water, ##H_2O##. A polyatomic ionic compound would be something like sodium chloride, NaCl.
We typically don’t talk about polyatomic because every ionic compound, by definition, has to have at least two atoms in it – a cation and an anion. What we do talk about are , which are groups of atoms that, together, form either cations or anions. The sulfate ion (##SO_4^(-2)##) is an example of this.