Interesting question! I think the idea of colonial relationships within the framework of the Ottoman Empire is a complicated idea, and one that deserves some more scholarly attention.

The simple answer to this question is no, Greece was not a "colony" of the Ottoman Empire in any way that would be recognizable to Europeans as a "colony". For nearly the entire time that modern day Greece was ruled by the Ottomans it was fully incorporated into the Ottoman state structure, and even as that structure changed to include a parliament, it was included (though it was also in the process of separating itself, so that's a little bit tricky). The point is, in terms of governance, there was basically no difference in the way the Ottomans ruled Greece from the way they ruled Bulgaria or Iraq or Syria.

Now, that alone doesn't mean the relationship couldn't have been in some way colonial. After all, once France took Algeria from the Ottomans, it was incorporated into the French state as a department, not a colony, but to say the relationship was anything but colonial would get you run out on a rail at any respectable academic conference. And the Ottomans did have governmental administrations that functioned somewhat like a colony. Many of the northern black sea districts were runs as vassal states, which could be seen as a form of colonialism, and the Anglo-Egyptian condominium of the Sudan, though run by agreement between the mostly independent Egypt and the British Empire, was technically still under the aegis of the Ottomans (and the Egyptians in charge at the time were as Ottoman as they come). But, Greece was neither a vassal state or a condominium, so I digress.

What would have made the Ottoman's relationship with Greece colonial? Well, if we accept colonialism as a dynamic in which a subject people are ruled by a foreign power without much or any say in their own governance, then maybe we can say it was colonial to a degree. In areas such as Greece, Christian populations (or 'non-Muslims' broadly construed) were likely in the majority (though not as big a majority as they might have today) and as such, for most of Ottoman rule, were unable to directly influence the affairs of state, including issues like warfare, taxation, courts, etc. Of course non-Muslims were allowed a certain amount of autonomy under Ottoman law to administer their personal status according to their own belief system (ie: the Greek Orthodox Church, headed by the Patriarchate in Istanbul) in exchange for an extra tax (known as cizye). In this sense, I think you could say that the dynamic between the Ottomans and any directly-ruled area that was comprised mostly of non-muslims had colonial characteristics. I know that sounds convoluted, but I think this relationship is an important one to understand because it does point up a power-imbalance between the citizenry and the state, one that was ultimately used as justification for both nationalist-separatist movements and European imperialist/colonialist moves against the Ottoman Empire in the 19th century.

Some extra food for thought here:

Eve Troutt Powell, A Different Shade of Colonialism

Timothy Mitchell, Colonising Egypt

Mark Mazower, Salonica: City of Ghosts