Your calculation is wrong: the number of strings containing 3 consecutive zeros is not $2^6$.
It would be $2^6$ if we demand that zeros are present in some particular 3 positions. For example, there are $2^6$ strings that starts from 3 zeros. Then each of remaining 6 positions can be filled with either 0 or 1, giving us $2^6$ possible options.
If you want to use this approach to solve your problem, you need to consider many options: there are $2^6$ strings starting with 3 zeros; there are also $2^6$ strings with zeros on positions 2-4; there are also $2^6$ strings with zeros on positions 3-5... etc.
But you cannot simply sum this up to get the answer. Because these sets are intersecting. For example, the string consisting of 9 zeros belongs to all of these sets (it starts from 3 zeros, it has zeros on positions 2-4 etc.) and so the string '000000000' would be counted many times. There are also lots of strings which are counted several times in this enumeration, for example, the string '000100010' was counted twice.
The correct approach is to use recurrence relations. Here is the idea: let $A_n$ denote the number of strings of length $n$ which does not contain 3 consecutive zeros. Then $A_n = A_{n-1}+A_{n-2}+A_{n-3}$.
Why is that so? Well, there are 3 options for a string of length $n$ that satisfies our condition. It may ends with 1, or ends with 10, or ends with 100. These options are mutually exclusive, and also they cover all possible strings. So number of strings of length $n$ is the sum of numbers of these three kinds of strings (ending with 1, ending with 10, and ending with 100).
It remains to note that number of strings of length $n$ ending with 1 is exactly number of strings of length $n-1$ satisfying the original condition, so there are $A_{n-1}$ of them. Similarly, number of strings of length $n$ ending with 10 is exactly number of strings of length $n-2$ satisfying the original condition, so there are $A_{n-2}$ of them. And similarly for strings ending with 100, so there are $A_{n-3}$ of them.
But before using the formula $A_n = A_{n-1}+A_{n-2}+A_{n-3}$, we need to calculate several steps manually first.
So, let's count now:
$A_1=2$, there are strings '1' and '0';
$A_2=4$, there are strings '10', '01', '00' and '11';
$A_3=7$, there are all strings of length 3 except '000'.
Then $A_4=7+4+2=13$; $A_5=13+7+4=24$; $A_6=24+13+7=44$; $A_7=44+24+13=81$; $A_8=81+44+24=149$; $A_9=149+81+44=274$.