Can a waterpatrol arrest a person for DUI or anything related if the boat has been docked and nobody was in the boat ?

Here's a statute that will help answer your question:  http://www.moga.mo.gov/statutes/C300-399/3060000165.HTM.

Based on the foregoing it appears that the dock was within their jurisdiction.  As for the boat being empty, " Each water patrol officer, while investigating an accident or crime that was originally committed within such patrol officer's jurisdiction...may arrest any person who he or she has probable cause to believe has committed such crime, even if the suspect is currently out of the water patrol's jurisdiction."

Looks as though they were within their legal authority to charge you.  However, I don't have all of the facts, to be certain of your rights you can speak to an attorney in your area that handles DUI cases.  This is a technical area of the law and perhaps they can either have the charge thrownout or reduced (and the penalties minimized). 

Although I do not practice law in MO, the general rule is that officers may arrest an individual if the officers have "probable cause" to believe that the suspect committed the crime.  Remember, the "probable cause" standard to arrest is much lower than the "guilt beyond a reasonable doubt" necessary to convict.  With respect to your question what this means, in a practical sense, is that it may theoretically be possible for law enforcement officers to obtain probable cause to arrest for a DUI-related offense without actually witnessing operation (i.e., through witness statements, etc); however, their reliance on alternative forms of evidence may make it difficult to demonstrate the "guilt beyond a reasonable doubt" necessary for conviction.  I suggest that you consult with and/or retain a criminal defense attorney to discuss the strength of the state's evidence as well as the merits of any and all potential defenses that may be available to you, in the interest of obtaining the most favorable resolution of this charge as possible.