Place the numbers by their size

The problem can be re-formulated in algorithmic style as follows: $$ \begin{matrix} a_0 = 1 & b_0 = 1 & c_0 = 1 \\ & & c_1 = 2^{c_0} \\ a_1 = 4^{a_0} & b_1 = 2^{b_0} & c_2 = 2^{c_1} \\ & & c_3 = 2^{c_2} \\ a_2 = 2^{a_1} & b_2 = 4^{b_1} & c_4 = 2^{c_3} \\ \cdot & \cdot & \cdot \\ \cdot & \cdot & \cdot \\ a_k = 4^{a_{k-1}} & b_k = 2^{b_{k-1}} & c_{2k} = 2^{c_{2k-1}} \\ & & c_{2k+1} = 2^{c_{2k}} \\ a_{k+1} = 2^{a_k} & b_{k+1} = 4^{b_k} & c_{2k+2} = 2^{c_{2k+1}} \\ \cdot & \cdot & \cdot \\ \cdot & \cdot & \cdot \\ A = a_{1000} = 2^{a_{999}} & B = b_{1000} = 4^{b_{999}} & C = c_{2000} = 2^{c_{1999}} \end{matrix} $$ Now we know how to calculate these huge numbers - though very much in principle :-)

The logarithm with base $2$ may be defined formally as $\,\operatorname{lg}(x) = \ln(x)/\ln(2)$ .
But in the practice below its meaning is much simpler, as might become clear from a few examples: $\lg(2) = 1 \; ; \; \lg(4) = \lg\left(2^2\right) = 2 \; ; \; \lg(8) = \lg\left(2^3\right) = 3$ . In general : $\,\operatorname{lg}\left(2^x\right) = x$ .
We need a function to chop off the exponent from a power (tower) of two. We could have called this function "chopper", but the proper name for it in common mathematics is $2$-logarithm. Take it, or if you don't like logarithms: leave it. The whole employment of our "exponent chopper" is like in here: $2^x > 2^y \; \Longleftrightarrow \; x > y$ . So what's the problem?

We are going to employ mathematical induction. To that end, define subsequent "approximations" of $A,B,C$ as follows: $$ A_n = a_{2n} \quad ; \quad B_n = b_{2n} \quad ; \quad C_n = c_{4n} $$ As the first induction step, we calculate: $$ A_1 = a_2 = 2^4 = 16 \quad ; \quad B_1= b_2 = 4^2 = 16 \quad ; \quad C_1 = c_4 = 2^{2^{2^2}} = 65536 $$ That's not enough to establish an inequality between $A$ and $B$, so we take a second step for these: $$ A_2 = a_4 = 2^{4^{2^4}} \quad ; \quad B_2 = b_4 = 4^{2^{4^2}} = 2^{2\cdot{2^{4^2}}} $$ Logarithms base $2$ : $$ \operatorname{lg}\left(2^{4^{2^4}}\right) = 4^{2^4} = 2^{2\cdot{2^4}} \quad ; \quad \operatorname{lg}\left(4^{2^{4^2}}\right) = 2\cdot 2^{4^2} = 2^{1+4^2} $$ And again: $$ \operatorname{lg}\left(4^{2^4}\right) = 2\cdot 2^4 = 32\quad ; \quad \operatorname{lg}\left(2\cdot 2^{4^2}\right) = 1 + 4^2 = 17 $$ From $\,32 > 17\,$ it follows that $\;A_2 > B_2\,$ , namely: $\;2^{2^{32}} > 2^{2^{17}}$ .

Now assume that $\;C_n > A_n > B_n \gg 1\;$ and prove that $\;C_{n+1} > A_{n+1} > B_{n+1}$ . $$ \begin{matrix} A_n = a_{2n} & B_n = b_{2n} & C_n = c_{4n} \\ A_{n+1} = a_{2n+2} = 2^{4^{A_n}} & B_{n+1} = b_{2n+2} = 4^{2^{B_n}} & C_{n+1} = c_{4n+4} = 2^{2^{2^{2^{C_n}}}} \end{matrix} $$ Taking logarithms two times: $$ \begin{matrix} \operatorname{lg}\left(A_{n+1}\right) = 4^{A_n} & \operatorname{lg}\left(B_{n+1}\right) = 2\cdot 2^{B_n} & \operatorname{lg}\left(C_{n+1}\right) = 2^{2^{2^{C_n}}} \\ \operatorname{lg}\left(\operatorname{lg}\left(A_{n+1}\right)\right) = 2A_n & \operatorname{lg}\left(\operatorname{lg}\left(B_{n+1}\right)\right) = 1+B_n & \operatorname{lg}\left(\operatorname{lg}\left(C_{n+1}\right)\right) = 2^{2^{C_n}} \end{matrix} $$ From which it follows that $\;C_{n+1} > A_{n+1} > B_{n+1}\;$ as well. Especially: $$ C_2 > A_2 > B_2 $$ So for all $\,n \ge 2\,$ we have $\;C_n > A_n > B_n$ . Now specialize for $\,n = 500\,$ and you're done.
Conclusion : $\;C > A > B$ .   Suggestive picture (not pretending anything more):

BONUS. Somewhat more of a challenge is the following modification of the question:
in $C$ there are $1500$ numbers $2$ (instead of $2000$). Then we have: $$ A_n = a_{2n} \quad ; \quad B_n = b_{2n} \quad ; \quad C_n = c_{3n} $$ And the first induction step results in an equality $\;A_1=B_1=C_1$ : $$ A_1 = 2^4 = 16 \quad ; \quad B_1 = 4^2 = 16 \quad ; \quad C_1 = 2^{2^2} = 16 $$ A second step is needed to establish an inequality: $$ \operatorname{lg}(\operatorname{lg}(A_2)) = 32 \quad ; \quad \operatorname{lg}(\operatorname{lg}(B_2)) = 17 \\ \operatorname{lg}(\operatorname{lg}(C_2)) = \operatorname{lg}\left(\operatorname{lg}\left(2^{2^{2^{16}}}\right)\right) = \operatorname{lg}\left(2^{2^{16}}\right) = 2^{16} = 65536 $$ Finally resulting in the same as before: $\;C > A > B$ .