How to get a list of logged in users,extension,

I'd prefer if there are a web API that can be used,

or if there is a desktop SDK that can be used,

is AES is the correct server to get this info from ?

Take a look at the first two of these search results.
https://devconnect.avaya.com/public/search/d_advanced_search.jsp?keywords=list+registered-ip-station&cbxCategories=faqs&r=1&B1=Submit

The information I'm looking for:

1- list of users(agents) logged in to receive or place calls [inbound/outbound].
2- list of extension that received/placed at least one call.
3- list of extensions and users(agents) logged in to these extensions.

the method:
1- using a webservice to access this info e.g. (http://anyip:2244/getallexts)

Numbers 1 and 3 can be achieved with the System Management Service (SMS) on AE Services. There is a free download of the SDK on the Devconnect Portal. Using a list operation on the Agent model will get you the information you seek for those.

As for number 2 in sticking with SMS there is a model called BCMSAgentReport that looks like it might give you the number of calls an agent has taken. I think there is some configuration on Communication Manager to enable BCMS reports. I haven't done much with reporting on CM but just to simply get the number of calls an agent has taken this looks like it will do it.

There is also an SMS test application included on your AE Services. When you download the SMS SDK there is a document call Usage.doc and this application is explained in there.

You will notice there isn't much documentation on how to use each and every model. It is expected that you use the SMS Test application in conjunction with a CM SAT session to find out for yourself how an SMS model should work.