As Zach points out in his answer, the dimension of this set is easily computed using Moran's formula. However, the dimension can also be computed via box counting, as the question specifies. The result, $\log(\varphi))/\log(3)$ is kinda of cool in its own right and there's a neat connection with Fibonacci numbers that arise when we compute the dimension this way.
Denote your set by $E$ and let $N_{\varepsilon}(E)$ denote the number of closed intervals of length not exceeding $\varepsilon$ required to cover $E$. Let's compute $N_{3^{-k}}(E)$ by inspection for several small values of $k$ and see if we can spot a pattern.
$E$ is a non-empty subset of the unit interval so, for $k=0$, we get $N_{1}(E)=1$. For $k=1$, we get $N_{1/3}(E)=2$; one of these sets must have length $1/3$ but the other need only have length $1/9$:

For $k=2$, we get $N_{1/9}(E)=3$; two of these sets must have length $1/9$ and one need only have length $1/27$:

It's a little harder to see but, for $k=3$, we get $N_{1/27}(E)=5$; three of these sets must have length $1/27$ and two need only have length $1/81$:

It appears that $N_{3^{-k}}(E)$ is always a Fibonacci number. In fact, if we index the Fibonacci numbers such that $F_0=F_1=1$ and $F_k=F_{k-1}+F_{k-2}$, then it looks like $N_{3^{-k}}(E)=F_k$. Let's call this a level $k$ cover. It looks like a level $k$ cover consists of two types of intervals depending on their length relative to $k$: $F_{k-1}$ type 1 intervals of length $3^{-k}$ and $F_{k-2}$ type 2 intervals of length $3^{-(k+1)}$. Suppose, for induction, that this supposition is true for a fixed $k$. Then, the $F_{k-1}$ type 1 intervals in the level $k$ cover decompose into $F_{k-1}$ type 1 intervals of length $3^{-(k+1)}$ and $F_{k-1}$ type 2 intervals of length $3^{-(k+2)}$ in the induced level $k+1$ cover. The $F_{k-2}$ type $2$ intervals in the level $k$ cover become $F_{k-2}$ type $1$ intervals in the level $k+1$ cover. Thus, the level $k+1$ cover has $F_{k-1}+F_{k-2}=F_k$ type 1 intervals and $F_{k-1}$ type 2 intervals for a total of $F_{k}+F_{k-1}=F_{k+1}$ intervals. We conclude that
$$N_{3^{-k}}(E) = F_k$$
for all $k\in \mathbb N$.
Now, it's well known that $F_k \sim \varphi^k$, where $\varphi$ is the golden ratio. As a result,
$$\dim(E) = \lim_{k\rightarrow\infty} \frac{\log(\varphi^k)}{\log(3^k)} =
\lim_{k\rightarrow\infty} \frac{k\log(\varphi)}{k\log(3)} =
\frac{\log(\varphi)}{\log(3)}.$$
Your calculation of the number of boxes is correct.
– Zubin Mukerjee Apr 06 '15 at 17:23$$\lim_{n\to\infty} \frac{\ln N(\epsilon_n)}{\ln(1/\epsilon_n)} = \lim_{n\to\infty} \displaystyle\frac{\ln(4^n)}{\ln\left(\displaystyle\frac{1}{1/9}\right)^n} = \lim_{n\to\infty} \frac{4n}{9n} = \log_9 4 $$
I think this is what OP did ... what exactly is wrong with it?
– Zubin Mukerjee Apr 06 '15 at 17:35