$$S_n=\sum_{i=1}^n\left((-1)^{i-1}\left(\sum_{k=1}^i\frac{1}{k}\right)\binom{n}{i}\right)$$
So, $$S_n-S_{n-1}=\sum_{i=1}^n\left((-1)^{i-1}\left(\sum_{k=1}^i\frac{1}{k}\right)\binom{n}{i}\right)-\sum_{i=1}^{n-1}\left((-1)^{i-1}\left(\sum_{k=1}^i\frac{1}{k}\right)\binom{n-1}{i}\right)$$$$=\sum_{i=1}^{n-1}\left((-1)^{i-1}\left(\sum_{k=1}^i\frac{1}{k}\right)\left(\binom{n}{i}-\binom{n-1}{i}\right)\right)+(-1)^{n-1}\left(\sum_{j=1}^n\frac{1}{j}\right)$$
Then, by this recursion relation, we get:
$$S_n-S_{n-1}=\sum_{i=1}^{n-1}\left((-1)^{i-1}\left(\sum_{k=1}^i\frac{1}{k}\right)\binom{n-1}{i-1}\right)+(-1)^{n-1}\left(\sum_{j=1}^n\frac{1}{j}\right)$$$$=\sum_{i=1}^{n-1}\left((-1)^{i-1}\left(\sum_{k=1}^{i-1}\frac{1}{k}\right)\binom{n-1}{i-1}\right)+\sum_{i=1}^{n-1}\left((-1)^{i-1}\frac{1}{i}\binom{n-1}{i-1}\right)+(-1)^{n-1}\left(\sum_{j=1}^n\frac{1}{j}\right)$$$$=-\sum_{i=2}^{n-1}\left((-1)^{i-2}\left(\sum_{k=1}^{i-1}\frac{1}{k}\right)\binom{n-1}{i-1}\right)+\sum_{m=1}^{n-1}\left((-1)^{m-1}\frac{1}{m}\binom{n-1}{m-1}\right)+(-1)^{n-1}\left(\sum_{j=1}^n\frac{1}{j}\right)$$
If you substitute $l$ for $i-1$:
$$S_n-S_{n-1}=-\sum_{l=1}^{n-2}\left((-1)^{l-1}\left(\sum_{k=1}^l\frac{1}{k}\right)\binom{n-1}{l}\right)+\sum_{i=1}^{n-1}\left((-1)^{i-1}\frac{1}{i}\binom{n-1}{i-1}\right)+(-1)^{n-1}\left(\sum_{j=1}^n\frac{1}{j}\right)$$$$=-\sum_{l=1}^{n-1}\left((-1)^{l-1}\left(\sum_{k=1}^l\frac{1}{k}\right)\binom{n-1}{l}\right)+(-1)^{n-2}\left(\sum_{k=1}^{n-1}\frac{1}{k}\right)+\sum_{i=1}^{n-1}\left((-1)^{i-1}\frac{1}{i}\binom{n-1}{i-1}\right)+(-1)^{n-1}\left(\sum_{j=1}^n\frac{1}{j}\right)$$$$=\sum_{l=1}^{n-1}\left((-1)^{l-1}\left(\sum_{k=1}^l\frac{1}{k}\right)\binom{n-1}{l}\right)+\sum_{i=1}^{n-1}\left((-1)^{i-1}\frac{1}{i}\binom{n-1}{i-1}\right)+\frac{(-1)^{n-1}}{n}$$$$=-S_{n-1}+\sum_{i=1}^{n-1}\left((-1)^{i-1}\frac{1}{i}\binom{n-1}{i-1}\right)+\frac{(-1)^{n-1}}{n}$$
Cancelling $-S_{n-1}$:
$$S_n=\sum_{i=1}^{n-1}\left((-1)^{i-1}\frac{1}{i}\binom{n-1}{i-1}\right)+\frac{(-1)^{n-1}}{n}$$
Then, given that $\binom{n-1}{i-1}=\frac{(n-1)!}{(n-i)!(i-1)!}$, $\binom{n}{i}=\frac{n!}{(n-i)!i!}=\frac{n}{i}\binom{n-1}{i-1}$, so:
$$S_n=\frac{1}{n}\sum_{i=1}^{n-1}\left((-1)^{i-1}\binom{n}{i}\right)+\frac{(-1)^{n-1}}{n}$$$$=-\frac{1}{n}\left(\sum_{i=0}^n\left(1^{n-i}(-1)^i\binom{n}{i}\right)\right)+\frac{1+(-1)^n}{n}+\frac{(-1)^{n-1}}{n}$$
By the binomial theorem, then: $$S_n=\frac{-(1+(-1))^{n-1}}{n}+\frac{1+(-1)^n}{n}+\frac{(-1)^{n-1}}{n}$$$$S_n=\frac{1}{n}$$
(please comment or edit for any corrections)