Modification indices can be requested by adding the argument modindices = TRUE in the summary() call, or by calling the function modindices() directly. The modindices() function returns a data frame, which you can sort or filter to extract what you want. For example, to see only the modification indices for the factor loadings, you can use something like this:

fit <- cfa(HS.model, 
           data = HolzingerSwineford1939)
mi <- modindices(fit)
mi[mi$op == "=~",]
       lhs op rhs     mi    epc sepc.lv sepc.all sepc.nox
1   visual =~  x1     NA     NA      NA       NA       NA
2   visual =~  x2  0.000  0.000   0.000    0.000    0.000
3   visual =~  x3  0.000  0.000   0.000    0.000    0.000
4   visual =~  x4  1.211  0.077   0.069    0.059    0.059
5   visual =~  x5  7.441 -0.210  -0.189   -0.147   -0.147
6   visual =~  x6  2.843  0.111   0.100    0.092    0.092
7   visual =~  x7 18.631 -0.422  -0.380   -0.349   -0.349
8   visual =~  x8  4.295 -0.210  -0.189   -0.187   -0.187
9   visual =~  x9 36.411  0.577   0.519    0.515    0.515
10 textual =~  x1  8.903  0.350   0.347    0.297    0.297
11 textual =~  x2  0.017 -0.011  -0.011   -0.010   -0.010
12 textual =~  x3  9.151 -0.272  -0.269   -0.238   -0.238
13 textual =~  x4     NA     NA      NA       NA       NA
14 textual =~  x5  0.000  0.000   0.000    0.000    0.000
15 textual =~  x6  0.000  0.000   0.000    0.000    0.000
16 textual =~  x7  0.098 -0.021  -0.021   -0.019   -0.019
17 textual =~  x8  3.359 -0.121  -0.120   -0.118   -0.118
18 textual =~  x9  4.796  0.138   0.137    0.136    0.136
19   speed =~  x1  0.014  0.024   0.015    0.013    0.013
20   speed =~  x2  1.580 -0.198  -0.123   -0.105   -0.105
21   speed =~  x3  0.716  0.136   0.084    0.075    0.075
22   speed =~  x4  0.003 -0.005  -0.003   -0.003   -0.003
23   speed =~  x5  0.201 -0.044  -0.027   -0.021   -0.021
24   speed =~  x6  0.273  0.044   0.027    0.025    0.025
25   speed =~  x7     NA     NA      NA       NA       NA
26   speed =~  x8  0.000  0.000   0.000    0.000    0.000
27   speed =~  x9  0.000  0.000   0.000    0.000    0.000

Modification indices are printed out for each nonfree (or nonredundant) parameter. The modification indices are supplemented by the expected parameter change (EPC) values (column epc). The last three columns contain the standardized EPC values (sepc.lv: only standardizing the latent variables; sepc.all: standardizing all variables; sepc.nox: standardizing all but exogenous observed variables)