Decide on a major. Many master's degree programs online are specific to a certain field of study so there is no reason to consider some schools as they won't offer the major you are looking for.
Do research online and find a list of master's degree programs which offer the major you are interested in. Make not of the cost of each of the schools at the same time as that will become increasingly important when you begin to finalize your decision.
Check the accreditation for the schools. Many schools have accreditations which are not even recognized in the United States. Other may have recognized accreditations, but they are not part of a regional accreditation. It is important for any master's degree programs online that they have a regional accreditation such as WASC.
Now that you have narrowed the list a little, start to look at the programs of the schools to see how it can work into your schedule. Most people are looking to get a master's degree online because they do not have time to go to a regular institution.
Check the schools for pre-requisites. You no doubt already have a bachelor's degree, but it will be important to see if there are additional classes that you will have to take in order to enroll and/or complete the master's degree programs online. Some states have different requirements so it may be better to look at one school versus another based on prerequisite courses.
Next narrow the list based on what you can afford. If they are too expensive, are they good enough masters degree programs online that you are willing to take out loans?
At this point you should be ready to make a decision and begin on your master's degree online.