Does concentration or pKa define acid strength? For example, is 3M HCl a stronger acid than 1M HCl? 

I would reason that the concentration of an acid/base does not influence its strength. Strength is determined by the pKa, and, as per Le Chatelier's Principle, the initial concentration does not influence the equilibrium constant.              

It may shift the equilibrium concentrations (meaning that the pH is higher for the 3M HCl), but it will not change $K_a=\frac{[H_3O^+][Cl^-]}{[HCl]}$ at equilibrium.

Is this right?
The term ‘strong acid’ is sometimes used in a rather fuzzy way and you ran into problems doing so. I prefer to use the term ‘strong acid’ only with respect to an acid’s $\mathrm pK_\mathrm{a}$ value and disregard all other influences. This gives a clearly defined measure of acid strength and we can easily sort various acids by their strength into stronger or weaker acids.

However, this is looking at the acid as a molecule. In real-life applications you are typically more interested in the property of a solution. To give a real-world example, imagine a $\pu{1M}\ \ce{HBr}$ solution and a $\pu{12M}\ \ce{HCl}$. solution. Obviously, $\ce{HBr}$ is the stronger acid, but the concentration of $\ce{HCl}$—also a strong acid and thus fully deprotonated—is higher. Therefore, the $\ce{HCl}$ solution is more concentrated or, as some would say, more acidic. It can do greater harm and it is able to protonate more Brønsted base molecules than its $\ce{HBr}$ counterpart.

If instead of examining a $\pu{1M}$ and a $\pu{12M}$ solution I had examined a $\pu{e-3M}$ and a $\pu{1M}$ solution, we could even base the discussion around the solution’s resulting pH: the stronger acid is much more diluted and will result in a solution of pH 3 while the weaker acid results in a solution of pH 0.