You have to be careful with numerical computations. If you are summing positive and negative values, you may get massive loss of significance. Perhaps an example will show what can happen. I use PARI/GP for the calculations.
First, define the $\ \eta(s)\ $ function in terms of $\ \zeta(s)\ $ if $N=0$ and using the double sum in equation $(3)$ if $N>0$.
Eta(s, N=0) = {if( N<1, (1 - 2^(1-s)) * zeta(s), sum(n=0, N,
2^(-n-1) * sum(k=0, n, binomial(n, k) * (-1)^k/(k+1)^s, 0.)))};
Next, try it with low precision and see how the values differ.
? default(realprecision, 19)
? forstep(n=50, 600, 50, print(n, " ", Eta(-9.5) - Eta(-9.5,n)))
50 -9.642528737400027361E-6
100 0.04774435040966354144
150 2.599876523165513738
200 -2.964487980721362893
250 256.1738173836702262
300 35.26046969887404046
350 -4458.254870234773912
400 -9841.293439755364521
450 75026.15715491652695
500 208518.5008905734908
550 249654.0022175838606
600 -194943.3625446287684
Now, try it again but with double precision and see what happens.
? default(realprecision, 38)
? forstep(n=50, 600, 50, print(n, " ", Eta(-9.5) - Eta(-9.5,n)))
50 1.36634363860781380424739243811E-17
100 -9.168029132151541870E-22
150 1.0314039806014013156E-19
200 -1.2323365675288983452001952305E-18
250 -1.07380641622270909181919052693E-17
300 3.2225691859129092780110367112E-17
350 -6.2902053300577065279589792889E-16
400 -1.1634529955480626497925160353E-16
450 4.6382289819863037395153447751E-15
500 8.4040100485998106924892434233E-15
550 -6.8760525356739577517253084299E-15
600 1.24908747773726136990750433575E-14
Notice the huge errors in low precision are gone in double precision. However, the errors still increase with increasing $N$ for a fixed precision. So what you need to do is increase both the precision and the $N$ to get convergence.
P.S.
For proof of convergence see the answer to MSE question 3033238 "Questions on two formulas for $\zeta(s)$" in case you are rightfully wary relying on limited numerical evidence.
For simplicity and generality make the definition $\,z := m^{-s}.\,$ Then your
three equations become
$$ -\sum_{n=1}^\infty a(n) \frac{n\,z^{-n}}{(z^{-n}-1)^2} =\frac{1}{1-z^{-1}},\tag{1}$$
$$ \sum_{n=1}^\infty \frac{a(n)}{z^{-n}-1} = \log\Big(\frac{1}{1-z}\Big), \tag{2}$$
$$ \sum_{n=1}^\infty \frac{\phi(n)}{z^{-n}-1} = \frac{z}{(1-z)^2}. \tag{3}$$
They all have radius of convergence $1$. For some background on series
such as these refer to Wikipedia article
Lambert series.
Best Answer
Use Euler's transform (ET)
For the Dirichlet Eta Function we obtain
\begin{align*} \eta(s)=\sum_{n\geq1}\frac{(-1)^{n+1}}{n^s}&=\sum_{n\geq0}(-1)^na_n&&;~a_n=(n+1)^{-s}\\ &=\sum_{n\geq0}\frac{(-1)^n}{2^{n+1}}\sum_{k=0}^n(-1)^k\binom nka_{n-k}&&;~\text{ET}\\ &=\sum_{n\geq0}\frac{(-1)^n}{2^{n+1}}\sum_{k=0}^n(-1)^k\binom nk(n-k+1)^{-s}&&;~n-k\mapsto k\\ &=\sum_{n\geq0}\frac{(-1)^n}{2^{n+1}}\sum_{k=0}^n(-1)^{n-k}\binom n{n-k}(k+1)^{-s}\\ &=\sum_{n\geq0}\frac1{2^{n+1}}\sum_{k=0}^n(-1)^k\binom nk(k+1)^{-s} \end{align*}
The accelerated series for the Riemann Zeta Function is listed here and a proof may be found here (Theorem $10.$ in particular). As far as I can tell the idea is similiar to the one given for $\eta(s)$.