There are two ways you can go:
Yes, there was a ruler, in the sense of a united state under one leader
Or
The Throne room was the residual area of the leader or chief (or religious ruler) of the palace at Knossos.
If we wish to precede with one(Two is just far too open ended, read some Castleden) then we have a few points of discussion regarding the gender of the ruler.
Shape of Throne: This one is the most common question posed regarding the gender of the ruler. "It is woman sized" they all say. I think this is best refuted by one simple comment; If i were the leader of a rich nation, and i had to sit on a stone throne often, then i would damn well want a cushion to sit on, pretty much rendering the size of the seat non-important.
Secondly, the ideal of Griffons being associated with females is to the best of our knowledge a Mycenean custom and is a rather weak point, as the depth of influence Mycenean culture had is really unknown. So we speculate this point.
The ideal of a mother goddess is so common and saturated in ancient culture and often has so little to do with the organisation of the ruling class it is hardly worth mentioning here, but again, speculation.
Take the writings of ancient writers with a grain of salt, as they are most likely biased by the ideal of a male ruler, and written in hindsight. But still, not using what is *somewhat credible* information is silly, and it wouldnt harm if you used it to make suggestions and not clear distinctions.
Other than this information, read lilems13's post, i just listed things not included and hopefully form your opinions regarding rulership.