One usually does not have this choice. When the LC is filed, the job requirements as indicated by your employer determine EB2 or EB3. If the employer indicated the JOB requires MS+0 or BS+5 or better, then it is EB2. Anything less is EB3.
Now it does not matter if you have more than that qualification. Whatever the JOB needs, the EB type goes by it. On the other hand, on the date of filing of LC, if you did not have ALL the qualifications indicated as required for the job, your EB application will be likely denied in I-140 stage.
Now assuming, you qualify for EB2, then go for it. EB3 has many more applicants, and hence you'll most likely end up waiting a year or more for a visa number to complete your 485 if you were to choose EB3