"It is a worth noting that.."
"It is worth noting that.."
The second sentence is unlikely to have a meaning in context.
Usually, people "note" something e.g. I note that you did not respond to my email. But for example, a government is an "it" and can note something. But when we use continuous tenses, the emphasis is on the activity, and the activity of noting (writing down or mentally recording) is usually done only by individuals.
"It is worth noting that" has a different meaning, because of the additional word "worth". The meaning is that:
"There is some value in noting that....."
The construction is "It is worth + noun/-ing"
If you love grammatical terms, "noting" in the first example is a gerund and in the second is a present participle.
1"It is a worth noting that.." Or 2"It is worth noting that.."
1 is bad English. 2 is good English.
2-like good sentences are... It is worth learning Spanish. It is worth sitting down in the waiting room. It is worth saying that she cannot work. It is worth typing that the computer's password is "open_sesame".... 1-like sentences are all bad. At least I cannot think of a good one.